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No need for the while loop...first remove everything that follows the comma on each line of the pattern file with awk and pipe its output to grep...
awk -F, '{print $1}' pattern_file | xargs grep {}...

The script snippet looks garbled. It sounds like the wildcard in the pattern got expanded by the shell at some point. You need more double quotes where it happens :)

But aren't you making it too...

Try

$ cat file
aaad_1577 64000
aaad_1577 72000
aaad_1577 72000
aaad_1577 65000
aaad_1577 65000
bbbd_2002 56000
bbbd_2002 57000
bbbd_3045 57000
cccd_3452 150000
dddd_6014 150000...

An awk approach that might work:
awk '
{
if ( R[$1] )
{
c = R[$1]
c = c + 1
...

Another smaller awk solution:

awk '
{
if ($1!=P) {
v[++C,0]=P=$1;
F=1;
}
v[C, F++]=$2
M=(F>M)?F:M
}
END {
for(j=0;j<M;j++) {
for(i=0;i<=C;i++)
...

Try:
awk '{gsub(/,/,"_",$1)}1' FS=XX OFS=XX file