I'm syncing my mac to another UNIX box and the sync fails, I get many failure messages.. why?

Depending on the files you sync and the protocol you use there are a large variety of errors you can get during the sync, especially the first time. Different UNIX systems have various levels of tolerance of certain filenames, character encodings, etc.. OSX is very permissive in filenames, for instance it allows very long file names with strange characters in them. Also, it is case preserving but NOT case sensitive. The other host you are syncing to may be much more limited. If you get errors, you should repeat the sync several times. If you keep getting failures always at a certain place, well, you may have to leave that folder out of the sync or try to change the source, or, if all fails and you cannot see what the incompatibility is, contact support with the error message, transcript, etc...

AASync does not sync some of my files.. why?

So you run the sync and the destination folder simply does not have some of the files?? Be sure to understand what sync mode you are using. If you are in default mode, the destination folder is not always checked, so a file is uploaded only if it has changed in the source folder! In a "normal" case the destination has all the files, so only the changed and newly added files are uploaded. So if you want to make sure all files are checked in the destination folder, be sure to check the box called "Always check destination folder" next to the Sync Mode button. That will force AASync to traverse through the destination folder every time to make sure your files are actually there. This is useful in situations where you have either changed sync settings or cannot be sure that the destination folder will stay intact between syncs.

Are there any situations where use of AASync is not recommended?

This is one of the most recurring questions. One must realize that a computer folder is not a telephone directory where contact records can be synced both ways. In a computer where files have naming conflicts and many other problems a two-way sync is not really feasable, it is simply to dangerous.
There is nothing to stop the user right now to set up two sync defs that are opposites of each other, that in fact would be a two way sync, but it is would not recommended at all! A two way sync is the fastest way to accidentally lose the files you are working on.
What is the solution then? It is to reorganize your work a bit... make sure you do not work on the same file on both locations, and if so, then use source code control like cvs or something similar. Name your folders/files differently in each location then you lessen the chance of files overwriting each other. The best way to deal with a two way sync is simply to avoid it altogether.

I have files in the destination folder that should not be overwritten if they are newer then the source! Is there a setting for this?

AASync cannot guarantee that newer files in the destination folder will not be overwritten. Why, because such a guarantee is simply not possible. You must realize that file modification dates cannot be compared between two different systems, since their time/date/timezone settings as well as clock states are different. Currently UNIX does not have a facility for this. Anybody who promises such a feature is simply lying. Not to mention the fact that FTP servers trash modification dates anyway, and even on an nfs or samba mounted external filesystems you cannot trust that the mod dates can be reliably compared with your client host. So, is there an answer? Yes. look the above answer and reorganize your work so backup/sync becomes manageable.

I am publishing our website through FTP. I get errors like this:
Failed to load folder /Volumes/MyProject/[08-145]website/web/images/thumbs, ignoring...

Two important caveats about backing up your files: You must make sure your source folder does not have unreadable folders, because they defeat the purpose of a backup sync. Also, you must consider that certain characters like quote, square brackets, star etc.. etc.. are legal on osx in filenames, but illegal in FTP, so if you want to back your files through ftp then those characters cannot be used in filenames in the source folder.

I have a choice how to reach the destination folder: a local nfs mount, FTP or SFTP. Which one should I choose?

SFTP is always the best choice. AASync will use an ssh shell, archivers and many other utilities to get the best result. It sounds strange, but an nfs/samba mount may not be the best choice, in many cases they impose restrictions, there are characterset problems and many other unforeseen complications. FTP is also very limited, it should be used if the other two protocols are not available.

My scheduled syncs are not executed when the time comes...however, if the GUI app is running, then the syncs do run on schedule.

When the GUI app is not running there is a completely different mechanism that executes the syncs. In these cases the cron daemon runs AASync in a GUI-less mode. If you move the app itself or the crontab entries have been deleted, that can cause scheduled sync executions to fail. If you have such problems, first try resetting something in the schedule like set it a minute later and save. That will rewrite the crontab and the schedule configuration. BE SURE TO SET THE SCHEDULE AT LEAST 15 minutes ahead of the current time!! If the sync still fails to execute, go to the sync's configuration folder (right click on the sync, select "Show Configuration Folder", or in the Finder navigate to YOURHOME/Library/Application Support/AASync_3.5/SYNCNAME ) there is a CRONLOG file which should get an entry similar to this:
ID:aadef_786308793_xxxxxxx_2047776792 Scheduled Sync Run at 2008-10-22 04:02:00 +0200, User:myuser, Console User:myuser
If this file is not there, or does not get an entry when the trigger time arrives, there is something wrong with cron, maybe there are permissions problems preventing execution of AASync.