Probably someone will tell you the bug, but that still makes this code hard to read, understand and maintain. Especially the multiple reads from $FILE are errorprone. And it really gets dark when your input file has an error in it.

My suggestion would be to rewrite this code as a state machine. A state machine has one variable with possible values of 0,1,2,3,.... That is the state. Whenever you parse something, for example a line with 'be0.01t' in it, you change the state to reflect where you are in the file. So state 1 might mean "I've just parsed a line with ####.30c, I'm expecting more of them now or blank lines or comments".

You might even draw a simple diagram now with arrows connecting two states, where one can lead to the other and note the condition on the arrow.

The new code would look somewhat like this:

my $state=0; #state 0 you expect a card id or comments
while ( my $line = <$FILE> ) {
    if ($state==0) {
        if ($line=~/.../) {
            dosemthing;
            $state=1;
        }
        elsif ($line=~/.../) {
            dosemthingelse;
            $state=4;
        else {
            print "error in datafile";
            $state=0;
        }
    }
    elsif ($state==1) {
        if ($line=~/.../) {
            ...
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The code will be more wordy but it will be a lot more mantainable and you will be more confident that your program can read whatever is coming at it