Baxi Solo 3 40 PF - flue issue?

Recently noticed that flue was not connected (leak of water through ceilling), initially thought, over 6 yrs it had separated. Once put together the boiler fired but stops every 6 secs. On seperating the flue again, it works perfectly. Boiler in airing cupboard (upstairs), flue goes up and then horizontal along loft to outside wall. Concern is that this seperation now appears was purposely done at installation (fortunately) due to the old flue going out roof (vent still there), we have not been a victim of Carbon M poisoning but does now explain symptoms of illness last xmas when in loft for 15 mins! Any ideas how we can connect flue without boiler keep cutting out.