Okay There are a few things I can mention that might give you a little assitance with your set up.
1) You should be able to run as many games as you would like on the memory stick as long as you have the room for it. You will want to make sure you are using ISO files and that the actual ISO is in the ISO files and not in folders in the ISO folder on the root of the memory stick.
It should look like this Ms0:ISO>Monster Hunter.ISO
I don't know why you are having this problem, I just thought I would give you the basic instructions on how to set up that folder. Someone else might know the answer to your exact problem if this doesn't help.
2) I have the same problem with my memory stick since I have a similar set up. So far I havn't had any issues and many others use a set up like this so you should be okay with that.
3) I don't know how you are running an ISO file with OFW installed because you have to have some form of CFW to run ISO's. Unless they have a signed ISO loader not sure about that.
There are some advantages to having CFW, you can just do alot more with CFW like back up your games to the memory stick and run homebrew. There is also much more that you can do.