You have several problems here:
1. Yummy FTP does not support AppleDouble
2. Your server does not support MacBinary
3. There is a 1 hour time offset between your Mac and your server
Since Yummy does not support AppleDouble it will treat all such files/folders as normal files/folders and sync them as such.
Since your server does not support MacBinary it won't de-code the MacBinary on receipt from Yummy, nor will it encode into MacBinary when sending.
So you're essentially trying to make the two 'talk' to each other in different languages. Which won't work, obviously.
Do your files actually have resource fork data that you need to keep? Resource fork and Finder meta data are very little used these days in Mac OS X. Bear in mind that MacBinary is an old format and is limited to files up to 2GB in size and limited to 63 characters in the file name. If not then a plain FTP file transfer will sort out this mess

The time difference is an easy one. In the sync setup window there is an 'auto-detect time offset' checkbox that you need to enable.
Also, I'm not sure why you need two Bookmarks? You could use one and choose Mirror to do a two-way sync.