I wasn't aware that VMS still exists!

I would first try to narrow down the bug. You said that this occurs with every Perl program. Since I don't know VMS, I don't know how DecTerm is supposed to behave, but maybe it's by design, that Perl takes over control. For instance, if you type at the command line (please adjust the quoting to the syntax on your platform; as I said I don't know VMS and the syntax on its shells):

perl -e "sleep 5"
[download]

it means that you can't enter anything for 5 seconds, but afterwards everything is fine again?

This would actually be the expected behaviour. On a xterm Window on Linux, this would be the same. I would have to start the program in the background in order to enter other commands while the Perl application is running.