I've tested as much as I can think of. Currently the issue stands that there's some sort of format error either with Paper/Shopkeepers/MC itself. The trade GUI is intermittently making items invisible. I've test through pack items, MMOitems, Vanilla items, etc. There doesn't seem to be much of trend. I can't pinpoint cause of this issue.

Hi, issues with invisible items are usually caused by one of your other plugins messing with item data packets.

Another user recently reported the same behavior and was able to track it down to soe feature of the Nexo plugin (glyphs in items). If you are using Nexo, try disabling this feature in their config (formatting > items).

If you are not using Nexo, you will have to do some testing to figure out which of your other plugins is interferring.