@lbusett Is the number of files+folders contained in the Insync folders same on both Windows and Linux?
If the number of files+folders in the Insync folder is large, the initial local folder scan every time you start Insync or do a pause-resume may take quite some time. This scan includes examination of every local file to see if it was changed while Insync wasn't running/paused. During this phase Insync would just either say "X items queued" or "Scanning for changes..." and minimal transfers would happen.
We are working on improving this. In the meantime, I suggest that if local files do not change when Insync is not running, you may skip the local folder when Insync starts:
1) Go to %appdata%\Microsoft\Windows\Start Menu\Programs\Startup
2) Right click Insync shortcut -> click Properties
3) In the "Target" field under the "Shortcut" tab append --skip-local-scan (See: https://drive.google.com/file/d/0B3IOdW-9p9oLN0hXWHhVS1kxOEk/view)
4) Click Apply
5) Perform steps 2-4 to for the other Insync shortcut too: %appdata%\Microsoft\Windows\Start Menu\Programs\Insync.lnk
This will make it skip the local folder scan to look for changes made while it wasn't running and hence it would proceed to the transfers faster. The changes that are done when Insync is running will continue to be detected.