I've got these devices setup, broadcasting 2x SSID's (one on 2.4 and one on 5Ghz) replicated to the AP902 via the AP management function on the 2860.

There doesnt appear to be any intelligence between the 2860's inbuilt AP and the 902, they seem to intermittently interfere with one another despite both being on auto channel select (no other AP's really in range so not like I have lack of channels here)

Has anyone else noticed that running the inbuilt AP with the external 900 causes issues, I've found the best way to stabilise things is to disable the inbuilt one, however the reason I bought a 902 in the first place was to extend range (house is over 3 floors)

Interfere in what way ??? You've not given any symptoms.

I was experiencing radio dropout on both 2.4 and 5Ghz, fine downstairs in range of the 2860 but upstairs where the 902 was covering (I've since returned the device for a refund after trying so many config variables) it would just drop completely. I used a survey tool to verify this, I was seeing both radios intermittently dropping out completely (wasnt my laptop I was using to survey as other nearby SSID's stayed up whilst this happened)

I also found that having the 2860 control the 902 wasnt as stable, config items would change when set and some things werent an option when controlled (eg: no auto profile for 5Ghz)

I have experienced this exact problem with my 2925n+ and AP902. I can't work out how to fix it!

Same here with 2925 and 902. Previously we had CISCO managed APs and these did not work with the 2925 so we purchased a mixure of 902s and 901c expecting that they would interoperate with the 2925 built in one, but they do not, and users complain of not being able to use WIFI so we had to disble the 2925 wifi profile - not it';s stable but we end up having to buy an extra AP.

They should co-exist, but yes, a Vigor 2925/2860 is the supported controller for the managed wifi system which uses the external APs. It isn't designed to use the built-in WiFi if you get one of those. You can lock the router away but have the APs optimally positioned.

If you are not using auto-configuration of the APs, you should turn that feature off.

Auto channel profile for 5Ghz is either now supported or should be soon.

http://www.draytek.co.uk/information/our-technology/wireless