/foldername/arma3server -cfg=/foldername/basic.cfg -config=/foldername/server.cfg -ip=ipaddress -name=public -world=empty -port=2302 -noSound "-mod=@a3mp;@a3mp_ap;@alive;@arc_gerup;@asdg_jr;@av_mods;@beton;@bovinton_tank_range;@brg_africa;@bullet_hits_value;@c17a3;@caf_ag;@cba_a3;@cho_f35b;@clafghan;@ctab;@everon2013;@fa18_a3;@fata;@fata_a3;@hafm_helis;@hafm_hmmwv_a3;@hafm_uaz;@hafm_uk;@hlcmods_core;@hlcmods_m60e4;@ibr_dtowns;@isla_duala;@j198_ftb;@kae_sz;@kio_l85a2;@kyo_mh47e_a3;@mas_usa_devg;@mbg_gen_afr_buildings;@mbg_killhouses;@mb_rocks;@mb_veg_adv;@mcc_sandbox_a3;@mk18_mod1;@nato_russian_sf_weapons;@nziwasogo;@opx_objects;@outlw_magrepack;@peral_a-10c;@pomi_pmc;@praa_av;@rav_lifter_a3;@razmisc;@rds;@rds_tank;@recoilfix;@rh_m4_a3;@rh_pistol_a3;@rus_spet_a3;@sangin;@sp_pack;@sthud_a3;@sti_a10_a3;@sud_russians;@super_flash;@task_force_radio;@uk_pack;@uk_sftg_a3;@usmc_a3;@vts_weaponresting"

If you copy the mod pbo files into a single mod folder structure, ie. @modname -> addons it works fine. Have tried with quotes and no quotes, still same issue.