The "old" version you are referring to didn't verify the integrity of the file transfers. Thus even if the problem happened there you wouldn't know unless you checked every single file.
I don't think the problem is related to the FTP client and I do not have any other suggestions than the one in my last reply.
Hello Mat -
You have your head buried in the sand. A search of "File size mismatch" on this forum shows that people are screaming about this and have been for more than a year. I have just spent an entire weekend beating my head against the wall trying to get v2.0.1001 to work. I don't think it is practical for you to go on a crusade to get the entire world to correct the problems on their web servers, since this is out of the hands of your customers. I have even seen 1 or 2 posts where the web server told the user that they already had the most recent version of the ftp server software. In my case, the host said there was nothing he could do about it, whatever that means, after I sent him a post from this forum (not this thread) which basically proved it is a problem with the server and not SmartFTP.
So, tonight, I installed WS_FTP and a 500 MB upload of large photo files and very small thumbnail files worked immediately and flawlessley on the very first try. The GUI is not nearly as good as yours. The logging is more cumbersome. In general, real-time information is not as good. Attention to detail is not as good. They don't have your (truly fantastic) transfer queue feature. It's just sort of klunky compared to SmartFTP. But, it works as long as my connection is intact and my kids don't log me off. So, after reading all these posts where you keep saying over and over that it's not your problem (which I believe) but you also do not provide a viable workaround that still allows me to take advantage of the features that discriminate you from your competitors, who do you think is going to get my 40 bucks at the end of my 30 day WS_FTP trial? I really wish it would be SmartFTP, but I am not encouraged after a year's worth of posts with no helpful solutions offered.