Comparing columns from two CSV files
First I'd like to call out the good things that you've done:


Writing functions, including a standard main().
Having more or less sensible function and variable names.
Proper use of with.


An improvement here is to stop parsing the file yourself, and to start parsing it with Python's native csv library. Even though your format is not technically CSV (it's separated by semicolon), you can still configure csv to use a different delimiter.

I recommend the use of the DictReader class. Given that you only pay attention to one variable, just use csv.reader. During initialization, get the index of the column you want, and then use that on every record that the reader gives back.

The critical performance issue here is that you have nested loops for row comparison. Given that you are comparing two series expected to be in the same order, but with edits (insertions and deletions), effectively you're doing a diff. Read this for a nice walkthrough.

http://www.xmailserver.org/diff2.pdf