I was having issues the last few days with activities not actually being loaded into Garmin Connect despite the message saying otherwise. I did some troubleshooting and found a workaround and am hoping it may be of some help to others.
Background:
Garmin Forerunner 610
Garmin Express Version 3.2.16.0
Apple OS X Mavericks (Haven't had the time to switch to Yosemite)
Solution:
I could not find the missing .fit files for the activities in the standard
home/Library/Application Support/Garmin/GarminConnect/XXXXXXXXXX/Upload/FIT_TYPE_4 folder.
I found files referring to my missing activities, but not .fit files, in home/Library/Application Support/Garmin/Express/Registered Devices/XXXXXXXXXX/PendingSyncUploads/FIT_TYPE_4. Note, the XXXXXXXXXX is whatever device you use. Mine just happens to be a 10-digit number.
I cut the files out and pasted into a blank folder on my desktop. This way if I needed them later I'd still have them. I then went through the menu on my watch to manually upload by going to the menu History > Options > Upload. I selected the activity that did not upload and selected "yes" when it asked if I wanted to upload. I waited for the file to upload and then went to Garmin Connect to see if it had in fact uploaded. It did!
My guess is that when Garmin Express tries to upload activities to Garmin Connect that it checks the PendingSyncUploads folder to see if there is anything new that needs to be uploaded. If so, it goes to the folder with the .fit files and checks there. Since the .fit files were missing from my computer it had nothing to send. Likewise, when I tried to manually upload the files from my watch to my computer it also checked the PendingSyncUploads folder to see if it had already transferred it. The files were still there so my watch would never re-send the activity.
I hope this helps.