I found this having just had the same issue. Dunno why it suddenly changed but I think I've fixed it!
In folder: Special K\Profiles\Saints Row, find the file SpecialK.ini. In the ini file, under [SpecialK.System] heading, change the line:
GlobalInjectDelay=0.0
to
GlobalInjectDelay=15.0
I found the launcher start-up takes about 10 seconds for me before the fullscreen game loads, so setting this to 15 seconds let the game start before Special K kicked in during the titles. As far as I can tell, it's working properly now.
Also, changing this seemed to fix the crash when I tried to open the overlay:
[Steam.Log]
Silent=false
to
Silent=true