I am not certain what the problem would be but I do not think it is the Improved Two-weapon Fighting Feat. I have made a couple of Ranger henchmen who had that feat and they never presented any unusual problems. I do remember reading somewhere (unfortunately a long time ago and I do not remember the details) that giving the Point Blank Shot Feat to henchmen can cause bugs, and IIRC most of the standard Ranger Packages hand out that particular feat. You could try editing packftrang1.2da (if that is the level-up package being used) so that PB Shot is no longer given, and see if that resolves the issue.
I have also run into an issue with the AI where henchmen who are stealthed or invisible sometimes seemingly get confused as to whether they are supposed to be hiding or fighting and thus just stand around doing nothing in combat. Not sure if that could be applicable here, but if your ranger operates normally with missile weapons I suspect it is something different.