Temporal Flux should tell you in the status bar at the bottom what the problem is. It will not open a file if it:
A) Is open in write mode by another program (like a hex editor)
B) Has a header and you decline to remove it
C) Does not have "CHRONO TRIGGER " as the ROM title
D) Is not version 1.0
Interestingly enough, it will open an interleaved ROM even if you decline to de-interleave it, which should probably not be the case.
---T.Geiger