I'm having the same problem with a Garmin 1000 and El Capitan. Garmin Express seems to communicate fine, sync, etc., except that I cannot send a course from Garmin Connect to the device. Garmin Connect "send to device" sees the Garmin 1000, but pressing send does absolutely nothing. Sometimes it tells me to connect the device to the computer and turn it on, but I also have the device wifi-enabled, and Garmin Express sees that the device is connected (whereas Garmin Connect does not).
I'm not having any major issues at all but have noticed a peculiarity. I have OS X El Capitan on my Mac. I have Garmin Express installed on my Mac and can connect my Edge 1000 cycle computer to my Mac with no issues - my Edge 1000 also has WiFi enabled and connected. When it's all connected up via USB, I log in to Garmin Connect and make some changes (to Training Zones, for example). I then click on 'Send to Device'. At this point I get a small popup window that says, "Waiting for device to connect".
However, Garmin Express has already woken up on my Mac and performed a sync to my Edge 1000 (which is connected via USB). Afterwards I've checked the device and the new settings are there. So it's clear that Garmin Connect is talking to my Garmin Express on my Mac.
The popup box in Garmin Connect that says 'Waiting for device to connect' mentions enabling WiFi on my device (it's already connected via WiFi). I just click on the X on the popup box to close it.
It seems that there is some comms failure between Garmin Connect and my device or Garmin Express. However, the sync is working fine.
