First, I saw your question and it made me curious. I have no idea why that is happening, but I am sure it is being done by Gmail, not Thunderbird. I suggest checking Gmail online to see if it is placing those messages elsewhere, such as the Important folder. And, just a reminder, the email will always be in Allmail.The question is to find why it is not also in the inbox, but elsewhere. My hope is that you will find the message online in a different folder and that may help you in resolving this. Good luck.

Thanks for your reply David but can't find solution on G-Mail site (can't even find All Mail folder there)

I think you need to click the all settings button in order to see it all. Then, on the message bar in Gmail is one for labels. That should show all the folders and their contents. I get lost on the Gmail site and stumble each time.

Thanks again David

Found the labels but this doesn't really show a path to All Mail folder. Also, the problem is intermittent which complicates it. Hopefully it might self correct with time