I'm developing a library for a led matrix shield (QuarterK) using Timer1 for refreshing the display.
It works just fine win 0019 & 0020, but when compiled with 0021 every other row is being dimmer than normal. It seems like something is creating additional interrupts at regular intervals making the time spent on some rows much shorter than others.
By tweaking the value of OCR1A I can change the position of the dimmer rows so I think it's confirmed. Will look into in further when I get home and have access to a oscilloscope so I can see the actual timing.
It can't be a gcc problem since 0020 & 0021 if using the same gcc version, so I think I'll blame the analogwrite() fix for pin 9/10 - it really can't be anything else according to the changelog - unless there are some other changed that escaped the changelog 
Edit:
Most likely it's my own d*mn fault for not initializing timer1 properly. The only change in 0021 that can affect this is the TCCR1B = 0; line in wiring.c