$TotalMatchesHash{$F,$BBEL,$AR,$VL} = $MatchCount;

This just concatenates the four variables and uses the result as a hash key. If they are all integers, you can't retrieve the previous values from that hash key unless you happen to know their lengths.

Update: That was actually wrong; see the other replies.

I strongly recommend to dump your hash like this:

use Data::Dumper;
$Data::Dumper::Useqq = 1;
...
print Dumper \%NewRFactorAverageHash;
[download]

This will escape non-printable characters in a meaningful way.