Hi sbonner,
I haven't seen the behaviour you seem to be experiencing, other than the design view not having all of data the generated report would have. This is due to the Generate Report action having the ability to filter data before the report is generated. A couple of tips I can think are:
1) Make sure none of the objects are outside of the boundries of the report. Even if a line or a text box is a pixel out of bounds, it can throw the layout of the report off.
2) Make use of the location and size fields on the property box. If you are dragging and dropping the objects, this area will allow you to more accurately place the objects. Lines and boxes can appear joined when in the designer, but are actually off when the report is generated.
3) For transaction templates, run some test transactions (estimates, invoices) to see how the reports look before sending out to customers. This can help if the data in designer preview might be different than the actual print preview.
Unfortunately, I haven't seen any other complaints about what you are describing. nor experienced this myself.
Hope this helps.
- Adam