Hello,
please, try to check what are you page and flypage values and it is possible you will need to adkust the preset variable filters in VirtueMart extension settings.
By default, there is ^[a-z.]*$, which means, that the URL will be SEFed only if in includes characters a-z or .; this means that e.g. flypage_new.tpl (or garden_flypage.tpl) will not fit into this rule becuase it includes '_' character.
So in such case, you will need to update the rule to ^[a-z._]*$ or ^[a-z._-]*$ if you want to accept "-" character also. (or you can delete the rules completely, but they are quite good proteciton before robots trying to hack VM)
We will update the rules in general in the next VM extension release.