Lightroom 3.4.1 changed Preference settings

I've been having colour issues with images I've uploaded to my lab for printing. It took some time to realize what had happened. The latest update of Lightroom reset all the Preferences for export in Photoshop. I was set to Adobe1998, 300 ppi and to work as a PDF. For some inexplicable reason I noticed the settings were changed to ProPhoto (colour space), 240 ppi and TIFF. I didn't change these. I've since reset the Preferences, but the problem is that I spent a significant amount of time editing several images in ProPhoto colour space (using Photoshop CS4). Is there any way to print the images with the colours I view (on a calibrated monitor) in tact? Converting the profile results in a very flattened colour space - olive green tinged and rather monochromatic. Any advice? Is this a common issue with LR 3.4.1?

Are you talking about the LR preferences for opening a file into PS? If so these are set in preferences, they don't include opening as PDF and should not be changed in anyway from those you set in preferences as this file is not changed when you update.
You can choose the colour space you require a file in during the export from LR and if you wish to attach a specific profile you can do this in the print module.
If you require a PDF then you will need to save as PDF from PS and you make all the colour settings and conversions in Acrobat for PDF's, not in PS or LR, as shown in the screen grab

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