i have had the same problems connecting 4x 290x on the mobo. after a lot of hassle i got them all 4 working with powered risers and the molex in mobo not used.

On another rig i used the molex on mobo to power and didnt use any powered risers. this gave far less trouble and is working stable ever since. The trick is not to use the 16x 16x riser at all. Just use 1x 16x on all gpu and no powered risers