It sounds like you have most of things working if you can get 1000-1100 lines of data.
If you posted some code we may be of greater assistance.
Form what you have said there appears to be a number of things that could be going on.
1) You are not reading the data fast enough.
2) Data is being currupted in transit.
3) File contents are being seen as flow control.
Posting code would help us answer if 1 is an issue.
Doing the copy from one machine to another next to it could help shed light on 2.
Create a huge file of all "A"'s could rule 3.
Ben