Batch plot layers incorrect colours

What I believe is happening is that when the files is opened in Print Organizer by default they are open in read-only mode and your level overrides are not being made. To change the Print Organizer behavior do the following:
In the pull-down menus select Edit->Preferences...
Remove check box from "Open design file in read-only mode". Restart Print Organizer.

Hello Ed,

Thank you for your help unfortunately I changed this setting and restarted the print organiser and it is still not working.

If you open your design file in read-only mode do you see the same behavior as in the output from Print Organizer.

Yes, if I open the file as a read only the colours are incorrect the same as the Print Organizer.

If you have the box unchecked in Print Organizer preferences, then are you using any custom command line arguments to start MicroStation?

Ed, I'll butt in here and add a little more,

There is no command line arguments. the levels update based upon the variable:
MS_LEVEL_AUTO_SYNC_ATTRIBUTE_LIST = ByLevelSymbology,OverrideSymbology,

When opening read only the levels display incorrectly, however even when opening and checking level attributes in read only the levels/colours etc show as being correct ie as per the library. My understanding of the MS_LEVEL_AUTO_SYNC_ATTRIBUTE_LIST variable was that upon opening the levels would be synced to the library(within that file), therefore when opening read only they should reflect the library settings?

Also by level and overrides colours are set to be the same. 

Ed, I'll butt in here and add a little more,

There is no command line arguments. the levels update based upon the variable:
MS_LEVEL_AUTO_SYNC_ATTRIBUTE_LIST = ByLevelSymbology,OverrideSymbology,

When opening read only the levels display incorrectly, however even when opening and checking level attributes in read only the levels/colours etc show as being correct ie as per the library. My understanding of the MS_LEVEL_AUTO_SYNC_ATTRIBUTE_LIST variable was that upon opening the levels would be synced to the library(within that file), therefore when opening read only they should reflect the library settings?

Also by level and overrides colours are set to be the same. 

I have set the variable - MS_PRINTORGANIZER_OPEN_DGN_READWRITE = 1 to override users settings in print organiser and force read-write which seems to have done the trick when printing at least.

Still have the issue of colours displaying incorrectly when files are opened directly as read only though

The issue here is the file is read only which means that no changes are being made to the file. This includes changes to the level symbology.

yes, I realise that, but why after being opened read/write does the change not stay in the file? so that the next time it is opened read only it appears how it should.

what happens if you do a "save settings" in the file while it is opened read/write ? and then open back up read only, do you see the changes ?

No change, the file still displays incorrect colours as read only.

We have save settings on exit set in preferences regardless so should never have to apply save settings. However, doing so makes no difference.