Yes (with conditions) - the saves changed from a .0 format to a .sav format somewhere around software v3.2, look at your saves if they are .sav - then yes they will work, if they are .0 then you have to change them (you can do this manually and they will work) to .sav
The only other issue I every have is sometimes the card will not accept the new SYSTEM folder, when you switch on it comes up black (but I had this with the original software too) then you have to back up, format the card and reload everything on
Check disc - it is checking the micro sd for fragmentation - I turned this off in the options
Skins - go to gbatemp.net in the forums / M3 Adapter / top sticky is Sakura - they have a whole range of skins you can add - and how to do it
Boot slot A - If you have a GBA Expansion card - the M3 one - it plays all gba games automatically no need to boot - if you have EZ expansion pack I am afraid - No idea
Most recent link is the site in my signature - this is the most recent but when you download it, it puts a program on the PC - select the top left hand option to get the software - this is a pain if you have a MAC or do not like to have programs on your PC - gbatemp will have the latest one but it usually takes a few days - with the latest official software you do not have the latest cheat database (its Dec) so you need to add that one too. The software you have will not play GTA Chinawars through Sakura you have to use touchpod - latest Sakura does.
Bigger file - if you don't have enough space it will crash.
Black screen - this is caused by poor contact in the ds slot - if you use the paper shim trick it solves this. For some reason Touchpod is not effected but Sakura is??
I always leave 1MB per game for making saves and the .opt file. I have 4 cards with Sakura - they all suffered from the black screen, I now open the M3 card - put a strip of 3 layers of insulation (electrical tape) on the back of the contacts to push them closer to the pins, reassemble, this had completely solved the back screen issue.
Now I generally format the card when adding the new software - back up, format, re install. Leaving the 1MB per game free space. Also if you have a big micro SD no more than 128 roms per folder, although you can make lots more folders. You can also change the properties of the SYSTEM folder, and make it hidden, making the screeen less cluttered.
Did you turn on soft reset - put the stylus on the game to play - push to the left and it starts - push to the right and you can turn on all the options
