You may experience intermittent uploads if you are:
Using a CF to SD Adapter
Please see the CompactFlash Card Adapter Issues article for more information on CompactFlash Adapters.
Out of range of your wireless network
Your Eye-Fi Card's wireless range for photo and video uploads is listed as 45 feet indoors and 90 feet outdoors. These values are under ideal conditions; camera bodies, walls, building materials, and other electronic devices can contribute to reducing your card's wireless range.
If you encounter wireless upload failures when your Eye-Fi card is in your camera, move your camera closer to your wireless router. Generally, your Eye-Fi card will upload without error if you are within 15-20 feet in line-of-sight of the router. Take several pictures and wait for a minute or two to see if the card uploads. If it still fails, remove the card from the camera and insert it into your computer with the Eye-Fi card reader; this will allow for maximum range since the card's antenna will not be constrained by a camera body.
Your camera's power settings have not been adjusted
If you are having difficulty transferring files while your Eye-Fi card is in your camera, check your camera's owner's manual and make sure that the power-management settings of your camera are adjusted so that it does not power-down immediately.
Most cameras have the ability to adjust the amount of time before the camera cuts power to the SD or SDHC card slot. Make sure to extend the amount of time the camera keeps power on to as long as possible via your camera's "Auto Power Off" setting. Doing so will ensure that the card has power when it needs to upload files.