Some obvious questions would be "what did you flash to it?" and "did you take a nandroid first so that you can easily undo the flash?".
A ROM flash cannot change how much storage or RAM a phone actually has, so it's tempting to wonder whether it's just confusing this app or whether it's really confused the operating system (it's not a port from a different phone?). What does the phone's system storage menu say about your storage? What does an alternative app (DiskUsage, Storage Truth, RAM Truth) say about this? If they give the correct answer then it's just this app that's not working with your ROM, but if they give the wrong answer then that ROM is badly messed-up.
But in any case if it's not performing properly I would suggest flashing back to the original software (assuming that you don't have a nandroid - in my ROM flashing days I would never flash anything without taking a nandroid backup first, and would always advise that to anyone contemplating modding their phone). This "reduced storage" is a sign that the ROM is incompatible in some strange way, but poor performance is quite sufficient reason to go back to what you were using previously.