If you attempt to duplicate a phase, the markup percentages nor checked settings do not come with it.

To Repeat:

1) Create a budget with at least two markup lines

2) Set Percentages and Check Box for "Show Percentages"

3) Create a new phase, duplicate the first

4) Observe how the percentages and previously selected Checkboxes do not copy

P.S. If there is somewhere else you want bugs reported, let me know.