Game bug or mod bug?

[r_wagner]

I understand this may have been covered before but I've had an issue with every new campaign (both with stock and gw+nygm+euc) that improvements fitted on my sub before the first patrol disappear after said patrol. Sometimes a couple of things (like radar and supercharger) have gone missing and the one time I docked at a milk cow everything was removed...

Anyone else seen this and know how to handle?

Thanks