Hello,
After upgrading from 5.5.0b11 my lights have almost stopped affecting lightmap bakes completely.
When I use mobile shader unlit (lightmap support), my scene was almost completely black. (i have about 50 point lights and 1 directional).
Only changing the lightmap atlas size 2048 to a smaller size started to help the issue. on 1024 i started seeing some more lighting, on 512 some more, and on 64 i think is all of them.
When i switch to standard shader even lowering the atlas size has no effect. my scene is black. 
I tried clearing the GI cache. Also tried 5.5.0f2. no luck.