@phaedrux
I think I've found the problem. The second tool I added to config.g had D1 instead of D0.
The printer only has one hotend and extruder so they are 'virtual' tools that let me change filament print settings (temp, retraction etc.) in the slicer.
; Tools
M563 P0 D0 H1 F0 ; define tool 0
G10 P0 X0 Y0 Z0 ; set tool 0 axis offsets
G10 P0 R0 S0 ; set initial tool 0 active and standby temperatures to 0C
;
M563 P1 D1 H1 F0 ; define tool 1
G10 P1 X0 Y0 Z0 ; set tool 1 axis offsets
G10 P1 R0 S0 ; set initial tool 1 active and standby temperatures to 0C