Hello Gary, as first, sorry for these troubles.
This is very strange behavior. In case you're using modules in several projects, module positions are stored in the main Skipper project file, so modules can be placed in different positions on every project.
Size and position of entities are stored per module, so this setting is shared in all projects.
But none of this should cause the behavior you're describing.
Would be possible to send us your project file together with module files so we can try to replicate and debug the issue here?
If so, please send it to [email protected]