Check the properties of the ROM files and make sure the archive checkbox is checked.
This is due to a bug in blargSnes's filesystem code. It will be fixed in the next release.
As for the next release, well:
* I thought I had got PICA200 rendering to work well, but not quite. It still flickered badly and overall not working well enough to be usable. I eventually did some investigation to find out what the GSP events were about and how to properly sync to the PICA200. In the end, it was worth it. Fast and stable display.
* Next step is, of course, adding the SNES video output to that. Probably not going to be too hard. Of course, there's the weird 3DS texture storage format coming into play, but I have ideas regarding that.
* The code behind the bottom screen UI is being rewritten. Internally, it's a lot easier to deal with, and will make it easier to add more UIs, config screens for example. A config screen would be nice for configuring things like scaling.
* With all that, two bugs in the new ctrulib have been fixed to this day. There will also be more, considering the whole 'return to home menu' part needs to be fixed.