In GSAK, goto GPS=>Setup..., under "GPS Brand" select Garmin; do NOT check "GPSr is USB" (even if you are using a USB to Serial adapter); select the Comm Port (Comm 1 generally, if using a USB to Serial adapter use the Comm Port assigned when you installed it); set the "Maximum waypoints for GPS" to 500.
To send waypoints, plug in cable, plug in GPSr (turned on), goto GPS=>Send Waypoints..., make the selections you want (or just check "Use Defaults") and click "Send".
Gave it a try without much luck. I did exactly what you said, and GSAK goes to "not responding." I never even get a dialog box like is shown in the Help menu example for GPSr Send in GSAK. After about 5 or 6 minutes I've been Ctrl Alt Deleting. I don't understand why it's doing that. I put a GSAK filter in place so that I'm only trying to put 30 of the 500 waypoints in GSAK into my GPS. I'm trying direct to serial without the USB adapter, by the way.