I'm not sure what method of uploading you were using - straight from the device or 'manual'. If it's the former, then it shouldn't be a problem going manual which is what I always do in Garmin Connect and RWGPS. Plug in the Etrex, switch to PC mode on the device, then open up RWGPS/Garmin Connect and go to the 'files on your computer' section and click through from there, you'll be able to navigate to the etrex and find the relevant file (it will be dated) when prompted. In Garmin Connect, there's a tab on the new upload page called 'manual upload' and just click through as above.
My apologies if you're already doing all that and it's not recognising it.