I have two separate issues with heavily modded game (CKAN lists 76 mods - http://utoopia.eu/img/test.ckan - list by Ckan). 1.0.5 worked well with around same set of mods.
1. Stations issue - One issue is with space stations only - and stations use some Near Future Construction 0.5.5 mod (cant upgrade because some parts are removed from 0.6 - maybe need to make new station - change central part with big docks to some alternative mod - and do savegame edit - but this is last resort). Currently sometimes station wobbles, trusses will go to infinite length, game wont allow depart from station and claim's its moving. On screenshot I noticed science lab is missing and seems to be away. Trusses are supposed to connect science lab to jet fuel tanks/engine pylons.
2. IVA everywhere issue - Other issue is with EVA and some satellites where IVA view is poping up behind kerbal on EVA or satelite core. Its quite disturbing - cannot see around - is Kerbal next to door already? Have to move around sideways to see more - IVA is only behind kerbal - so moving sideways allows to turn IVA to side also to take fewer space from screen. Also - kerbal portraits from right-lower corner are missing. Issue came some 2-3 days ago, probably because some mod updates arrived to CKAN.
Edit: IVA issue seems to have been fixed a day before 1.1.1 update by some mods.
In prerelease game was working fine, mods were just not working (depite being there). Issues are raising now with updates.