What is your transfer mode set as, Is it still set at AUTO?
Based on the log you provided FlashFXP is not sending TYPE I which is required, otherwise the files are transferred in ASCII mode. As you assumed the files do appear to be transferred in ASCII mode, its quite obvious from the log file.
SIZE is returning the ASCII size not the BINARY size and thats why it doesn't match.
Are you using 4.0 build 1548? If not you should be.
https://oss.azurewebsites.net/download
There are currently no known issues with transfer mode switching and I have not been able to reproduce this issue myself.
Can you please mail a copy of your flashfxp.ini to support@ at our website, From your flashfxp.ini I'll be able to determine if its a configuration issue.
One other possibility is that you may not be using an authentic release of FlashFXP, If that is the case please download an authentic version of FlashFXP from our website.