I've recently encountered problems (using Core FTP Lite version 1.3) when uploading an html file. Some of the code is missing once uploaded. Out of 16 lines, all very similar to display a thumbnail and link, about 10 were missing.
All of the missing lines of the code had one thing in commom a height value of 80. When I changed this to 81 the page uploaded complete!
I then had a similar problem with another file where it stripped out the lines referring to an image with a height value of "90". I changed it to "91" and it uploaded no problem.
Is is Core FTP or could it be my Firewall?