Why do you not see each other often? Just because you have your kids if you've been going out for a long time together and you've discussed moving in and getting married one day then shouldn't she be spending time with you and your kids rather then not see one another for a long time?
My guess is that she's getting bored with you and she's not bonding with you like she would if you were not so "part-timing" the relationship. Perhaps she feels resentment that she has to tell someone her artinerary that hasn't advanced their relationship?
The bottomline here is you have asked her to let you know when she's not going to be home to receive your call and she's not respecting that very simple request. Whether she's having an affair or not, she's certainly not valuing you enough to make you feel more secure that she loves you and wants you to be happy. That alone is something to think about and get resolved. You might as well put it all out on the table and figure out if you need to move on or something just needs changing up.
“The willingness to accept responsibility for one’s own life is the source from which self-respect springs.” ~Joan Didion