I am sure this is not correct and that the navigation buttons should be re-enabled!
Not necessarily. It depends on how you save and whether you are going through the form or a BO. When you Save, whether on a transaction or not, through a BO, the forms maintenance toolstrip will not be updated. However, if you call Save() through the form then you will get different results.
when I open a winform in Visual Studio 2005 from the project, the size of the form opens smaller than when I saved the form?
This has something to do with your development environment. Giving you a concrete answer on this one is not easy 
However, I have seen this before and it had to do with code in a Load or a New() that was manipulating the form size. In these cases you need to test on Designmode before executing the code.