JiffyDOS uses $9b to indicate if the function keys are active or not. Any non-zero value of P8ZP_SCRATCH_PTR will result in the JiffyDOS funciton keys being disabled when the Prog8 program exits. This occurs with or without %zeropage dontuse since it is a required ZP location.

This behavior of JiffyDOS can be verified by simply pressing F1 to see that it tries to load a disk directory.
Then do POKE 155,1 and try F1 again. It will do nothing.
Do POKE 155,0andF1` should be back to normal.

Currently P8ZP_SCRATCH_REG is using $03 which according to Mapping the Commodore 64 is part of $03/$04 or "ADRAY1" which isn't used by BASIC. Locations $5/$6 are listed as "ADRAY2" and also state they are not used by BASIC.

I would propose using $4/$5 for P8ZP_SCRATCH_PTR since ZP bytes 3/4/5/6 appear to be unused by basic. We are already using one byte from the ADRAY1 vector so I think using the high byte and a byte from the ADRAY2 vector would be better than interfering with JiffyDOS.

Using the following with VICE didn't show any use when running a few basic programs.

break load 0002
break load 0003
break load 0004
break load 0005
break load 0006

I would propose the following patch:

--- a/codeCore/src/prog8/code/target/zp/C64Zeropage.kt
+++ b/codeCore/src/prog8/code/target/zp/C64Zeropage.kt
@@ -9,7 +9,7 @@ class C64Zeropage(options: CompilationOptions) : Zeropage(options) {
     override val SCRATCH_REG = 0x03u     // temp storage for a register byte, must be B1+1
     override val SCRATCH_W1 = 0xfbu      // temp storage 1 for a word  $fb+$fc
     override val SCRATCH_W2 = 0xfdu      // temp storage 2 for a word  $fd+$fe
-    override val SCRATCH_PTR = 0x9bu     // temp storage for a pointer $9b+$9c
+    override val SCRATCH_PTR = 0x04u     // temp storage for a pointer $04+$05

And equivalent changes for the tiny C64 custom target.