Hi Dom,
Unfortunately the (long) information you attached to your post does not help much to understand your problem.
It is always extremely difficult to pinpoint a problem which, as you state in your report, sometimes happens and sometimes does not happen. It's up to you to try and find out what was different in those cases, so that we can have a diagnostic.
Here are a few ideas and queries for more relevant info.
Which version of Moodle are you using?
Did you recently upgrade your Moodle?
Are you using the very latest version of Questionnaire?
Did you have that problem just on ONE questionnaire on your Moodle site or on more than one?
Tell us about the settings of the "problematic" questionnaire: does it have more than one page? It is set as Save/Resume answers?
Is it a public questionnaire created in one course, then used in other courses on your Moodle site?
When you write "...we have started finding that teachers are claiming to have completed the questionnaire and yet we dont get SOME of those answers, other results ARE coming in."do you mean:
a- you are getting the responses from some respondents (teachers) but no responses from some other respondents
b. OR you are getting, for all or some of the respondents, all of their responses in the questionnaire OR only some of their responses?
For those teachers who "claim to have responded", have you checked their activity report in the Moodle course where that questionnaire is located? In the activity report you can view the exact timestamp where they submitted the questionnaire.
The more relevant information you give the better the chances are that we can help you, but again, the worst case to diagnose is when something "sometimes works and sometimes does not".
ATB
Joseph