Somewhat related to my other topic about TG16 output resolution problems, some games require you to hold down buttons and restart the system to switch them into high res mode:
http://www.tg-16.com/arcade-mode-high-resolution-shmups.htm
When you reset the system in RetroArch, if you are holding down any buttons it will halt the emulation until you release them, and only then will it restart.
An option to disable this behavior would be useful.