Happening in Sega Model 2 emulator, Supermodel and Mednafen as well.
I've been experiencing this same issue, only discovered it in the last few days. Coincided with upgrading Windows OS along with LB 10.10. Prior to upgrading I keep my PC offline (which is dedicated just for running LB) so periodically connect to run updates while taking my own a back up of my LB folder just in case. I've concluded this one is definitely a windows issue. Tried a bunch of graphics driver clean-up utilities but nothing effective unfortunately.
Tried rolling back to LB 10.9, .8.7.6. etc, all installations get tripped with the same issue... a few seconds into running a sega model 2 game like daytona USA i get through the first few seconds of selection screens and then big box pops up in front. Audio continuing and the emulator running the task bar. I tend to notice if play other emulators first like PSX, or retroach and then comeback to try model 2 or model 3 it will run stable, as before. So this seems to be an issue at worst when the PC is freshly booted. I have a bigbox running the startup menu to launch me straight in.
Undoubtedly a windows OS update-induced issue, which can't be rolled back. Will try Jason's suggestions tonight on the taskbar. If there's any logging utility you would recommend i install which logs processes running i would be happy to try that and report my findings back to this group.
Spent about 5-6 hours on this already. If i can get this fixed it will be lesson-learned on connecting to receive any any windows updates from now on! Thanks