I've recently upgraded to Photoshop CS5.1 and I've encountered that the pen tool will only let me fill in one path at a time. Older versions of photoshop would fill in all the paths at the same time so I don't see why the pen tool would be capable of doing that in a newer version.
Any help to fixing this would be greatly appriciated!
It should still work the same in photoshop cs5.
What version of photoshop did you upgrade from?
These are paths and not shape layers?
What are the settings in the tool options bar before starting the paths?
Have you selected the Path Selection Tool to see what the paths are set as i.e add, subtract, intersect or exclude?
Could you post a screenshot(s)?