When you die and get the buy previous ship dialog it doesn't remember your weapons groups.

(sometimes)

upon further investigation, it happens with older ships. As in, I've had a ship sitting there for a year and then I use it, when I go to buy back my weapon groups are gone.

I looked into this and it happens if you change your weapon groups and then launch without changing menus.
The weapon group info is sent to the server when weapon group screen is hidden (either by changing to a different tab, or opening the Options menu, etc...) for a network optimization. It's probably not as useful of an optimization these days.

So for now, the remedy is to change to a different tab or open the Options menu or something before launching.
Or when you launch, you can dock and then launch again and that will save the info.

I could add a 'Save' button next to the 'Clear' button which would flush the info to the server.

This is a new problem though, it didn't happen before a recent update (not sure which one, but two weeks agoish). Couldn't you make it autosave the groups every time you change them?