By the looks of it you have verifySignatures on. Can clients connect to the server without a problem?

in the /home/servers/arma/name/arma3/@aia/addons folder are there the bisign files? like this:
/home/servers/arma/name/arma3/@aia\addons\buildings_c.pbo
/home/servers/arma/name/arma3/@aia\addons\buildings_c.pbo.keyname.bisign
/home/servers/arma/name/arma3/@aia\addons\roads2.pbo
/home/servers/arma/name/arma3/@aia\addons\roads2.pbo.keyname.bisign
....

Do you have the bikey file of the mods inside the
/home/servers/arma/name/arma3/keys folder?
like:
/home/servers/arma/name/arma3/keys/keyname.bikey

Because you use linux:
Also make sure the file/folder names are all lower case. (no uppercase at all)

Normal players can connect just fine, only the headless client gets kicked.

Of you turn verifySignatures off the headless client works just fine.

I assume the headless client can't find his bisign files because of the slash.

Ralpha, yes to all

verify is 2;
All clients can connect just fine.
I can connect as a client using @aia. I transfere that EXACT pack to the server, and start the HC.
HC gets kicked. I don't.

I've resigned ALL of the files in @aia folder and transferred them along with the bikey. I can connect, HC gets kicked.

I remove @aia from the HC modline, it can connect just fine. Add it back, kicked.

There's no uppercase anywhere.

Could you make a screenshot of the server files and the HC files so I can have a look. screenshots will do or a treeview will also do as well.

You can use the command 'tree' for this:

1. install the 'tree' command
2. use 'cd' to go to your folder

3a) use 'tree' to show the view.

3.1) copy past this into a file

3b) use 'tree > treeview_arma.txt' and it will create a file that contains the treeview.

4. upload the file here.

I'll take a look where the problem is.

Here some info about tree-command: http://www.cyberciti.biz/faq/linux-show-directory-structure-command-line/

Ok, uploaded file.

HC files are shared with the server

I don't see a problem with the structure or files.
The only thing that could be the problem is if the bisign files are not up to date with the pbo file. So to solve that you can re-key the files. You can check them with this: https://community.bistudio.com/wiki/DSCheckSignatures
Or you can make your own bikey.
https://community.bistudio.com/wiki/DSCreateKey
https://community.bistudio.com/wiki/DSSignFile
All programs you need are in https://steamdb.info/app/233800/

You also have some files that have 2 keys for some files:
structures_e_c.pbo
structures_e_c.pbo.aia_tp_lite_2015_01_01.bisign
structures_e_c.pbo.fp_agm_150309.bisign

Do give you a bit of info if you don't know: a bisign file is a check-sum for the pbo, if the pbo changes the check-sum doesn't match up and the server will notice this and kick you out. So if you change a pbo you need to re-key it.

Other then that, but are not any problems:
@aia doesn't exist but checked @aialite for this.
and the \ slashes in the first post are also not the problem.

Let me know if the problem is fixed after re-keying the pbo.
so 2 solutions:
1a. check the pbo with the bisign (DSCheckSignatures) (if invalid go to step 2)

2a. make your own key (DSCreateKey) (you can also just do this)
2b. make new bisign keys (and delete the old ones) (DSSignFile) (check if solved)

I hope this will fix it. Let me know if you solved it.

No, re-signing does not fix it from my experience. If the keys were the issue that would mean clients would have issues with connecting too, and they don't have any.
I assume the headless client can't find his bisign files or something similar.

It's a bug with the Linux Arma server, thus this bug report.

Does it only happen with some mods or all mods? Could you upload or link a mod that has this problem so I can confirm it?

@Ralpa, thanks for your help. I think you're missing the first part of the problem description, I'll explain it more out below:

Problem: SOME bisign files does not work. From my tests, only happens to All in Arma Terrain pack Lite (@aiatp, @aialite) addon. As soon as it is disabled, everything works fine, that is, other addons are running aswell. CBA, AGM, TFAR, RHS, and more.

What I've tried so far:
1 Pre-setting:) Server has the latest AiALite including bisign and keys

2. WORKS: Connect to the server from my computer as a CLIENT using the full AiA addon
3. WORKS: Download the AiALite addon folder from the server, and connect from my computer as a CLIENT

4. BROKEN: Connect the HC using the same AiALite as the server is running (and was downloaded)
5. BROKEN: Upload the full AiA from my computer (that I could connect with as a client) and let the HC use that

6. WORKS: Resign the keys for AiALite, check them using checkSignatures, connect from my computer as a CLIENT
7. BROKEN: See 6) and upload the new bisigns including .bikey (also including deleting the old bisigns)

Note that having multiple .bisign files for one PBO does not matter, only one need to match.

The problem seems directly linked to AiA TP, full and lite version AND running a Linux server.

I've asked other Linux server owners if they could run HC and AiA but I've found none that do.

Still broken. This seems directly related to the amount of mods loaded and the order they're loaded in. It will complain about random pbo's but if i move the mod order around, it'll change pbos the HC gets kicked for.

Still broken.

This page https://forums.bistudio.com/topic/140621-arma-3-headless-client/page-14
and forward will show more people using LINUX having the same issue.

Still broken, perhaps related?

http://feedback.arma3.com/view.php?id=27172

Did some testing for the bisign issue
running @CBA, @ACE3, @CUP_Terrains = it works just fine. that's a total of 486 pbo's (we've moved some pbo's around).

Adding @acre2 to the modline (52 files), it'll break and bisign doesn't work anymore. (HC is kicked, complains about vanilla A3 pbos)

An uneducated guess would be that 512 pbo's is the max before HC starts breaking due to invalid bisign files

Would REALLY like this to be fixed.

In my case there is 549 *.pbo files. I will try to check with less amount, but yeah, this seems to be an issue.

Thank you @cuel for info. I removed some stuff from my modpack, ended up woth 505 pbo files (but not all actually used, ie optionals in ACE) and HC started working.

Nope. It times out after some time and not booting into game, sadly. But at least it passes signature verification (it seems)

Still broken.

I seem to have counted the .bisigns aswell, so the actual number would be 256