I for the test did that code,
works for me:

fileA:
A
AA
ABC
ADF
BFD
EFF
ZFF
ZZD

fileB:
exchangeA_groupA.gateway_risk=A 10 10 AA 10 10 ABC 10 10 ADF 10 10 EFF
+ 10 10 MMM 10 10 NDB 10 10 RFD 10 10 ZFF 10 10
exchangeA_groupB.gateway_risk=A 10 10 AA 10 10 ABC 10 10 EFF 10 10 MMM
+ 10 10 NDB 10 10 RFD 10 10 ZFF 10 10
exchangeA_groupC.gateway_risk=A 10 10 AA 10 10 ABC 10 10 EFF 10 10 MMM
+ 10 10 NDB 10 10 RFD 10 10 ZFF 10 10
exchangeB_groupA.gateway_risk=A 10 10 AA 10 10 ABC 10 10 EFF 10 10 MMM
+ 10 10 NDB 10 10 RFD 10 10 ZFF 10 10
exchangeB_groupB.gateway_risk=A 10 10 AA 10 10 ABC 10 10 EFF 10 10 MMM
+ 10 10 NDB 10 10 RFD 10 10 ZFF 10 10
exchangeB_groupC.gateway_risk=A 10 10 AA 10 10 ABC 10 10 EFF 10 10 MMM
+ 10 10 NDB 10 10 RFD 10 10 ZFF 10 10
exchangeC_groupA.gateway_risk=A 10 10 AA 10 10 ABC 10 10 EFF 10 10 MMM
+ 10 10 NDB 10 10 RFD 10 10 ZFF 10 10 ZZD 10 10
exchangeC_groupB.gateway_risk=A 10 10 AA 10 10 ABC 10 10 EFF 10 10 MMM
+ 10 10 NDB 10 10 RFD 10 10 ZFF 10 10
exchangeC_groupC.gateway_risk=A 10 10 AA 10 10 ABC 10 10 EFF 10 10 MMM
+ 10 10 NDB 10 10 RFD 10 10 ZFF 10 10
exchangeD_groupA.gateway_risk=A 10 10 AA 10 10 ABC 10 10 EFF 10 10 MMM
+ 10 10 RFD 10 10 ZFF 10 10
exchangeD_groupB.gateway_risk=A 10 10 AA 10 10 ABC 10 10 EFF 10 10 MMM
+ 10 10 NDB 10 10 RFD 10 10 ZFF 10 10
exchangeD_groupC.gateway_risk=A 10 10 AA 10 10 ABC 10 10 EFF 10 10 MMM
+ 10 10 NDB 10 10 RFD 10 10 ZFF 10 10

script:
open IN, "<fileA" or die $!;
        %fileA = map {/$/; $` => 1} <IN>;
close IN;

open IN, "<fileB" or die $!;
while($line = <IN>){
if($line=~m/(exchange[BC]_groupA)\.gateway_risk=/){
        print "in line $1:\n"; $line = $';
        foreach $key (keys %fileA){
                print "\tnot found $key\n" if !($line=~s/$key//);
        }
}
}
close IN;


result:
in line exchangeB_groupA:
        not found BFD
        not found ADF
        not found ZZD
in line exchangeC_groupA:
        not found BFD
        not found ADF
[download]

now I'm gonna test your code. Will put update with the results.
UPDATE
result of your code on my machine:

Use of uninitialized value $sym8 in string eq at ./b.pl line 39, <DATA
+> line 4.
A       exchangeB_groupA(ln4)   not found
A       exchangeC_groupA(ln7)   not found
Use of uninitialized value $sym8 in string eq at ./b.pl line 39, <DATA
+> line 40.
ADF     exchangeB_groupA(ln4)   not found
ADF     exchangeC_groupA(ln7)   not found
Use of uninitialized value $sym8 in string eq at ./b.pl line 39, <DATA
+> line 52.
BFD     exchangeB_groupA(ln4)   not found
BFD     exchangeC_groupA(ln7)   not found
Use of uninitialized value $sym8 in string eq at ./b.pl line 39, <DATA
+> line 88.
ZZD     exchangeB_groupA(ln4)   not found
[download]

P.S. did you get the job?