I had this problem twice now. My activities recorded by my Garmin Forerunner 310XT are not uploaded to Garmin Connect. However, they show in Garmin Training Center (the Windows application). Here is what to do.
1. Look in the C:\Users\<username>\AppData\Roaming\GARMIN\Devices\nnn\Garmin Connect\Pending Uploads folder. If the activity files are there, the first one is probably “poisonous”. (The file name contains the date in ISO (yyyyMMdd) format.) You can in fact check that by trying a manual upload in Garmin Connect (the web site). (But if you use Internet Explorer 9, you must switch on compatibility view to be able to upload.) If the manual upload results in an error message saying “An error occurred with your upload. Please try again.” there is something wrong with the file. (Trying again won’t help.)
2. Move the “poisonous” file to another folder, or delete it.
3. Record a new “dummy” activity and press reset. This will trigger a new upload. Hopefully, all your pending uploads will upload and disappear from the pending uploads folder.