Matt Finish problems

You might be forced to gloss the model again then matte coat it.  The gloss should give you a good surface for the matte coat.

Yep, sounds like your flat base/clear mix wasn't thoroughly mixed, or you used a tad too much flat base. (generally speaking, more than about 25% flat base can ruin your day)  It's pretty easily fixed though - a light coat of straight clear gloss will fix it and then you'll have to flat-coat again.

You might keep an eye on the humidity in the air - I can remember having problems like you refer to spraying Dullcoat out of a spray can on warm to hot days when there was also high humidity present.