As I work at home despot let me point out that in MOST spray paints, matte does not equal flat. It's actually between flat and sateen, or satin, depending on who made it. if you want flat, buy dull coat, or something similar. hope this helped.
I find that I'll seal certain parts of a figure with Krazy-Brand liquid type Superglue (other bands just don't dry smooth... ugh), then seal the whole figure with Vallejo brush-on Matte varnish. I've never encountered a 'shiny' effect after it's applied. It actually levels out how the figure reflects light amazingly well.
this also happens to me sometimes.. if I spray on too much matte sealer, the surface becomes smooth and shiny... kinda like semi gloss... maybe you should try spraying just a small amount of it... a few very short bursts instead of one continuous spray. that usually does the trick for me. hope that helps.
Cheers,
-Blayne