In this case, I can tell you definitively, Eclipse is not part of the problem: you should be able to execute that command on the command-line and get identical results.
When Perl encounters a use (or require) statement, it might subsequently do a lot of compiling, as it processes not only these modules but all of their direct and indirect dependencies. A syntax-error anywhere can produce this result, with or without Eclipse or any other IDE.
If you do not get identical results, check your local PERL5LIB and other settings to make sure that they really are identical to those that are established in the relevant (Eclipse ...) settings. You can be quite sure that you will find some discrepancy there.