Are you using managed workspaces in ProjectWise or local workspaces? If you plot the same data outside of Projectwise, do you get your linestyles?
In general, if using a managed workspace in ProjectWise and the dgn displays correctly when opened from ProjectWise in MicroStation, IPLOT should pick up the workspace information as well and plot correctly. One instance when this may not occur is when the MicroStation set as the print engine is not integrated correctly with ProjectWise or not the same MicroStation used to display the file when opening from ProjectWise. A good test is to open Microstation from the menu or desktop, do you get prompted to log into ProjecWise?
If using local workspaces, is it possible that you are using some other configuration when opening MicroStation such as a shortcut referencing a -wc option? If you are using a customization for MicroStation, you have to make this same information available to Interplot by defining this same information in iplot.cfg, IPLOT_MSENGINE_OPTIONS.