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looks good - should work.
Please address Don's ask in post #8 before proceeding any further.

works on the sample files you gave me. there must be something different with your actual files - and not just the size.

do cat -vet patternFile and post a sample output here (using code tags).

a bit verbose, but....
awk -f ah.awk patternFile inputFile
where ah.awk is:

FNR==NR {
f2[$0]
next
}
{
for(i in f2) {
if($0 ~ ("^"i))
beg[i]++
if($0 ~ (i"$")) {
...