First, welcome to TFL. Second, you have a License to Carry a Handgun, not a Concealed Weapons Permit. Semantics, maybe, but it does make a difference. I digress...
Just wondering, how do you know the money order was CASHED? I strongly doubt your MO was cahsed the day after you submitted your application for an LTCH. I have heard of people waiting quite a while for their LTCH's to come in. I don't see where you should have any issues with passing your background, since you did get your 4 year license. So my guesses are as follows:
1) Wrong address in their system, possibly due to a discrepency between your previous address on file and current, or error reading your application.
2) Someone with a similar name got in serious trouble, and they have to do a deeper background check to conclude it isn't you.
3) They're still working though a backlog, and your MO was cashed somewhere closer to March-April.