AVR-Chat

>
>        But, if I apply an external reset, all goes back to normal.  
>        A 100nF capacitor from RESET pin to ground solves the problem, too.
>        Does the internal PowerOn Reset is not working on Timer2?
>
>        Any suggestions?

Do you fully init the timer, or do you leave some of the registers at defaults?

While Atmel has been very good at providing sane powerup values, I have always been nervous about relying on them.  In general, I try to fully init any peripheral that I use.

Also, check how you handle reset. 

I've had problems in the past, initting SPI too soon after reset.
This was an interaction with the device programmer, but you might be seeing something of that nature.