This is not an Amiga problem but a PC one. Connecting two Amigas with a nullmodem cable works like a charm with Copy or Type to and from SER:.
Only if you send data from a PC to an Amiga the last buffer does not get transferred. The best way to override it is to enter Ctrl-C on the Amiga side when it locks up and then sending the data again. The Amiga side will then return to the Shell but the transfered file will be smaller or larger than it should be.
Perhaps this text helps you:
http://homepage.uibk.ac.at/homepage/c725/c72578/amiga/adfsenderterminal/methods.htmlBye,
Thomas