You have made my week! The aim for MonkeySqueeze is a script that installs with the minimum of fuss and does the intended job. Quite a bit of time has gone into fixing bugs, install issues and writing the user guide to help make the process as painless as possible. I'm not suggesting its perfect but it is nice that MonkeySqueeze is doing what you want, as you say:
no sync lag, no install problems, no hassle - just works. Brilliant!!!!
I'm also glad that you find MediaMonkey impressive. It is fantastic as a music/media management system and when you combine it with Squeezebox the package is near unbeatable.
I too have a combination of mp3 and FLAC files. Initially I made do with mp3s due to size limitations but as storage sizes have increased I am gradually changing over to FLAC as I would like the best quality when playing music on my HiFi. However as you say you cannot tell the difference when playing both formats on computer speakers or the like.
Are you getting any lag in the music between MediaMonkey and your Squeezebox devices when playing FLAC files? I find there is a lag of about 6-7 seconds on my system which means the occasional track is cut off at the end when the next track starts to play. That is the next major issue to address in MonkeySqueeze and I'm finding the feedback on the matter to be very helpful in making future decisions to rectifying the issue.
Regarding your two issues, I'm at a loss to understand how MonkeySqueeze can cause those problems, however I've burnt myself previously by making rash statements only to be proven wrong at a later date, so I'll play this one low key. Is the synchronize issue related to the synchronize function in Squeezebox Server,or is it the one in SqueezePlay? Have you recently upgraded the server or SqueezePlay that might cause this issue? Might need a little more info to take this further. I don't have a Touch so I can't try and replicate the text issue but it maybe related to SqueezePlay if you are syncing direct from it. SqueezePlay is more than a music player and it can control a lot of other things beside music. Let me know what you find.
Thanks again for your much appreciated comments and I'm stoked you found the MonkeySqueeze experience to be fantastic.