Hi there,
I had the same thing happening when I started to assemble my first rack just about three months ago. I am using the Synthrotek Deluxe Power with two of the Noise Filtering Distribution Boards. After having installed just a few modules (way below what the Deluxe Power can handle power-wise), the -12V LED and the LEDs on the modules were constantly flashing and the system became unusable. After lots of testing I figured out that the WMD Pro Output module was causing this.
I hope the guys at Synthrotek don't mind if I post the response I got from them after asking for help via email, since this might be helpful for you as well:
Reply from Synthrotek: "I believe what you are experiencing is the power influx when you first turn on the system. Each module has capacitors in it that need to charge, so when a module is first turned on, it will draw more current than what they will when they are running. I believe that the Pro Output may just have a large influx, or really big caps that take a lot of juice to fill up, and the Deluxe Power module may not have been able to keep up with how much it wanted."
This was most likely what was happening in my rack, since the WMD Pro Output has two insanely large capacitors on its backside. Since removing the Pro Output, I didn't have any problems with the Deluxe Power anymore.