A sneaking feeling tells me that you will shortly be Suffering from Buffering. (There is a similar warning in IPC::Open3.) Namely if there is, for instance, a long error statement, you may be trying to read from its STDOUT while it is waiting for you to check its STDERR. This might take a while...

You are likely to need the select command or its OO wrapper IO::Select to do this properly. (I think you will find IO::Select easier to figure out.)