> My fosc is 32 MHz.
> By using a 32 bit prescaler i get 1MHz

I think you mean divide by 32. And your instruction clock rate is
only 8MHz, not 32MHz. A /32 pre-scaler reduces this to 250kHz
(= 4us per count)

> I let the timer fire an interupt on overflow and reload it with 0xffff -
> 0x3E8

So, your count rate is 250kHz and you're loading Timer0 with -1000d
= a rollover rate of 1000*4us = 4ms, or x4 the time you expected

> But this give the wrong result. Instead if I change the prescaler to 4
> the timing is OK

I'm not sure if I've missed something in your description :

A /4 pre-scaler puts the count rate at 2MHz = 0.5us/count. 1000
counts would = 0.5ms. It would appear to me that a /8 is needed
to produce a 1MHz count rate = 1ms from a 1000 count

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