Let's break it down piece by piece:
何をいっているか → What are you saying?
However, depending on the context, this can sound a bit to harsh or direct (Japanese people tend to avoid this). As you may know, adding the
の makes this less direct and/or rhetorical.
何を言っているのか → What are you saying? (not expecting an answer; not so direct)
Now, add in the
何を言っているのかわからない → "What are you saying?" is what I don't understand → I don't understand what you're saying.
かもしれません is an ending for low probability, i.e., "may" or "might".
何を言っているのかわからないかもしれません → I may not understand what you're saying.
けど I think could mean one of two things in this case. Like the other answers said, it could be that it means "but" and there will be a follow-up sentence. However, what seems more likely to me is that it is another "softener" to bring more indirectness, and take focus off the listener.
Take these sentences for example:
- 言いたいことがあるんだ → "There's something I want to say to you" → Sounds very direct, almost confrontational, putting the listener on the defensive
- 言いたいことがあるんだけど → "There's something I want to say to you..." → Sounds less confrontational; "softens" the statement; no reason for the listener to become defensive
Now in that sense, let's look at your sentence with and without
- 何を言っているのかわからないかもしれません → Direct and curt; Sounds like they're implying "I might not understand what you're saying (you nonsense-babbling idiot!)"
- 何を言っているのかわからないかもしれませんけど → Indirect; non-confrontational; almost like "(Excuse me but,) I may not understand what you're saying."
So adding those two structures makes the translation closer to something like "Hmm, I'm afraid I may not understand what you're saying..."