I see. You're saying the example output shows only middle parts of lines. Well...

Thinking logically, there are four possibilities:

1. Bug in your program
2. Bug in your tool that you use to view the output file
3. Bug in Perl
4. User error

So,

1. I don't see any apparent bugs in the snippet you provided. Although some things are strange, for example, if ($nbGABlocks == 0) {... doesn't seem to have any effect, since @arrayToPrint is emptied before appending more elements anyway (in the NORMALBLOCK loop). Bugs are not impossible, but they must be somewhere else...
2. How are you viewing the file?
3. That kind of bug in Perl seems unlikely... What is the Perl version?
4. Yeah, how are you viewing the file? For example, you're opening the file for appending, are you making sure you're viewing the new part and not the old one?

There is a number of 'paste your code here' sites on the Internet, e.g. hastebin.com. Would it be possible to paste the output of Data::Dumper and of your program using it or a similar site? And more of your script, too (ideally something that we could actually run).