Would be interresting if you could measure the frequency on the clock pin on the sid-chip. (That Clock is called "Phi2" on Pin 6 on the SID-chip.
I know that this clock is different depending NTSC or PAL Version:
The Clock on PAL machines is (312 * 63 * 50) = 0,982800 MHz
The Clock on NTSC machines is (263 * 65 * 60) = 1,025700 MHz
In the Datasheet of the SID 6581 is a Table for the Clock of 1,000MHz: The value for 880HZ (note A5) is 14764 for the 16-bit value that you have to write into the frequency-register of the SID.
If you have the PAL version the chip is slightly slower, so you (or your software) have to use higher values.
If you have the NTSC-Version the SID works a little bit faster, so you (or your software) have to use lower values.
( I think there are correct formulas out there in the internet to calculate the right frequency for PAL or NTSC)
Also there different Frequencies for the notes - depending if the note scala is tempered or mathematically evenly distributet (with SQRT(12)-Steps).
Usually you use the "well tempered" (i don't know the right english term for that) frequency-scala for the notes so that combinations of them sound "right".
If you have measured the wrong clock on your SID-Chip you may change the crystal in your system to a new one and maybe also the capacitures around them to get a stable correct clock frequency that does not change over temperature.