Nope, not just you, apparently a bug when using auto-pilot in SC. There are bug reports already.
And ninja'd by Factabulous.
It happens without SCA too. I just tried the game, updated and started without issues. Then I got my Eagle from storage, bought an Advanced DC (interestingly I could buy both, a DC and an ADC, which is more expensive) and left dock. Using auto undock worked fine, and outside I checked my module settings. I usually give weapons 2, fuel scoop and SRV hangar a 3 (no SRV on Eagle), and 4 to Cargo Hatch. My settings were fine, as before the patch.
Flew around a bit, scanned wakes near the port, and since I use 102% for all modules, the Cargo Hatch was disabled when deploying hard points.
Entered SC, flew around looking for USS (in my home system). Btw. it seems there are now more HGE, I found 3.
Returned to port, dropped from SC (no SCA!) and all modules were at 1. Had to fiddle around manually to deploy and scan 2 wakes. So it happens always when entering or leaving SC. Bug report filed.
One thing, if anybody has seen this too: Before the patch it was possible to assign any priority to a module. so I could give 4 to the Cargo Hatch even if all other modules are at 1. This seems impossible now, you can only give it 2. Makes no sense at this time, since it is reset anyway.