www.jfileupload.com

Given the following relevant parameters:
mode=ftp
resume=true
overwrite=false
retry=99
template=":filename:-:timestamp:"
preprocessingfilter=archiver

1. Selected file(s) to upload are compressed into a single ZIP file.
2. Timestamp is appended to ZIP filename.
3. Upload commences.
4. Network connection failure causes applet to retry.
5. Network connection re-established within 10 retries causing applet to attempt resumption of upload.
6. Timestamp previously appended to filename replaced with new timestamp.
7. Resume logic uses filename (with new timestamp) causing LIST command to look for non-existent file, then proceeds to upload newly renamed file from beginning.
8. Upon upload completion, destination contains partially uploaded file (with the original timestamp) and complete file (with the new timestamp).

Has anybody else experienced this issue?

That the problem with timestamps. Could you see if another option could fit to you need in template parameter:
http://www.jfileupload.com/products/jfi ... _http.html