I'm using GDrive, HiDrive, SkyDrive and a few other storage providers in combination with BoxCryptor.
A tool like rsync is used to synchronize a sort of work-directory-tree (external harddisk) to the GDrive / SkyDrive / etc directory on a computer.
The work-directory-tree consists of 1000's of files.
In case of HiDrive we use the rsync protocol to synchronize the directory tree directly to rsync.hidrive.strato.com
The result is that only changed files are synchronized by GDrive, SkyDrive, etc.
We haven't noticed any GDrive synchronization problems, as said, only changed files are synchronized to whatever storage provider.
Under Windows + Cygwin we use something like
rsync -rvt --progress -e ssh source_path/work_dir/ destination_path/work_dir/
sometimes in combination with the -n or --delete command line argument.
Please note the rsync source and destination '/' at the end.
See for example:
and in particular
for the abovementioned rsync command line options.
I don't think that your synchronization problems are due to GDrive, but don't hesitate to prove me wrong ;-)
Hope this is of some help ...