Works for me.

$source = 'VM';
$COB = '20080605';

for (qw(
   VMTKSWPDCN0120080717.TXT
   VMTKSWPSLN0120080717.TXT
   VMTKSWPDLA0120080717.TXT
   CMVMCSHFEN0120080605.TXT
   VMTKSWPDLN0120080605.TXT
   VMTKSWPTVN0120080605.TXT
   VMTKSWPSLN0120080605.TXT
   VMTKSWPDLA0120080605.TXT
   VMTKSWPTVA0120080605.TXT
   VMTKSWPDCN0120080605.TXT
   VMTKSWPSLA0120080605.TXT
)) {
   if ( /^$source.*$COB/ ) {
      print("$_: match\n");
   } else {
      print("$_: no match\n");
   }
}
[download]

VMTKSWPDCN0120080717.TXT: no match
VMTKSWPSLN0120080717.TXT: no match
VMTKSWPDLA0120080717.TXT: no match
CMVMCSHFEN0120080605.TXT: no match
VMTKSWPDLN0120080605.TXT: match
VMTKSWPTVN0120080605.TXT: match
VMTKSWPSLN0120080605.TXT: match
VMTKSWPDLA0120080605.TXT: match
VMTKSWPTVA0120080605.TXT: match
VMTKSWPDCN0120080605.TXT: match
VMTKSWPSLA0120080605.TXT: match
[download]

Make sure your variables ($_, $source and $COB) contain what you think they do. Specifically, look for trailing newlines that need to be chomped.