This is not a bug related to your bag, but to do with a certain combination of items in your inventory. It seems like the master server tries to sort your items when you switch between servers and sometimes it is unable to make everything fit: If you have a small number of spaces left, sometimes the reorganisation will fail to make the right shape available, and when it finishes it's sort task it is unable to make objects that require multiple slots in specific horizontal or vertical combinations fit, and so it discards them.

The fix is that it must apply the logic of storing and restoring to your bags based on the number of slots they use, starting with the largest.