I suggest that you factory reset your Alt-F DNS. Do this by pressing the reset button for 20+ seconds.
If it still doesn't work, then I suggest removing the hard disk drives (mark each drive for which slot they were in) and power it on again. This way it will only be running from the Alt-F firmware rather than possibly loading something incompatible from the disk.
Regarding your lights on your router when you plug in the network cable, I assume you are referring to the link speed lights by the port connection. The solid yellow color may be normal for your router, you would have to look up the manual for your router to interpret it. Yellow may indicate that the auto negotiation gave it a 100 Mbs link speed, possibly due to using a CAT-5 network cable. If you have a CAT-5e or CAT-6 cable, then you should be able to get 1 Gbp speed (possibly a solid green LED for the link).
Tom