Hi,
3rd party extensions usually causes conflict when working with another 3rd party extensions.
The shipping plugin you are using, and CleanMart. Essentially they are both 3rd party extensions to VM and they are developed to work with Default Virtuemart Component. When they are combined all together, it is most likely there will be some conflicts.
We have used AJAX loading to load the shipping rate, which usually conflicts with 3rd party shipping/payment plugins. This AJAX should be disabledt. There is a parameter in the "Flexible VM3 Template" plugin to easily disable this AJAX loading feature:
Try disabling this parameter:
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and see if this fixes the problem.
Regards