I just replaced the rear pads on my '05 and discovered the inner pad was hanging up on plate. Removed the pad and filed it enough to clear and reinstalled it. Never have I seen this before but it was real. I used EBC sintered brake pads.
Make sure the brake caliper piston is functioning properly. Remove the caliper, remove the pads, remove the plastic that fits in the piston, check for debri and remove if there is any. Lightly press on the rear brake pedal while checking to see if the piston moves. The piston should move easily. Push the piston back in the caliper.
How bad was the fluid you flushed?
Rear brakes are never as effective as front brakes. Agree with the comment about the brake line but you should be able to tell if it is bad by looking at the brake line since it will be swollen and maybe just in a place or two. The inside of the brake line will break down and restrist the brake fluid flow.
2005 KLR 685
2015 Yamaha Super Tenere ES, 5/23/2015
2012 Yamaha Super Tenere; Purchased 7/30/2011; Sold 5/23/2015