I hadn't even thought about the tube from the dispenser. As it happens I couldn't get much down there to clean it though. As you suggest I'm going to re-wash/proof. Thanks for the advice.
It's also handy to know what to do when it gets moldy.
I noticed Gortex say on their website not to use wash-in proofing. I suppose Nikwax know what they are doing. They replied very promptly to my emails. Here is what Nikwax say on the matter. The first is from Nikwax UK and the other from Nikwax USA.
"Thank you for your e-mail enquiry.
Detergent residue could effect the reproofing process in two ways. Firstly, it could cause white marks to appear on the fabric- and secondly the durable water repellency may not be very effective. You can check for this by spraying/splashing some water onto the Bivy bag. If the water beads up into little droplets which can be easily shaken off - the proofing is fine. However, if the water soaks straight through - it will need to be reproofed again!. If you reproof twice in succession on fabric that it is already waterproof - it can leave it very waxy and stiff!
Best regards,"
"Don't worry, you may not have gotten the absolute best waterproofing but you should still have gotten good results. There is no harm in reproofing it again right away, but too save you money, I would recommend waiting until your jacket shows signs of "wetting out" before going through the cleaning and proofing process.
Next time, definitely try to remember to clean the dispenser first.
Thanks for checking with us, I wish you well in your outdoor adventures.
Cheers!"