Using lpr send the file to the print server, which should be CUPS which has it's own mechanism for converting PDFs suitable for the printer, but can be different to Evince and Adobe Acrobat Reader as they are three separate implementations.

You may be able to influence the CUPS engine via the CUPS website: http://localhost:631/

Adobe Acrobat Reader is likely to be the most accurate and you can force it to send a completely rasterized image to the printer.

Evince has pretty much no tweaking available.

edit: CUPS uses pdftops and friends to print PDF documents, this is based on Xpdf which is the same ancestry as Evince.

Adobe Acrobat Reader includes additional options to attempt fixing background colours and an option that hints that it is your printer messing up the final copy:

Well it seems Adobe has turned its back on the Linux community so I have to update this answer. I suppose you have moved to the latest Ubuntu or at least one that can use the more capable open source applications below.

Viewers With Annotation Viewing Capabilities

Open source viewers

Okular

A KDE based application, runs ok and looks ok in Gnome, one of the best open source applications that can both view and create annotations, note that this application can do standard and non standard annotations. You can create annotations that can be viewed by all viewers that support the pdf standard for annotations.

you can create annotations that does not interfere with the document, you will need to use Okular to view these, these can then be converted to standard annotations if you need to.

Evince

The default viewer on Ubuntu and most Gnome based desktops, the latest now have a somewhat limited support for standard pdf annotation viewing.

Proprietary Solutions

PDF Studio Pro

A very good fully capable PDF viewer and editor, from Qoppa Software, there are trial versions available for standard and pro, the pro verson has most of the features of Expensive tools from Adobe.

• Redaction, block out parts of documents you do not want people to see.
• OCR, Make scanned pdf searchable
• Digital Signature, sign documents adding image of signature.
• Create and fill forms
• Measure Tool, measure using scale factors, CAD type dimensioning.

Kami (Formerly Notable PDF)

Kami is a browser based solution, can view standard annotations, can create non standard annotations, this works with Google Chrome browser, you can save annotated PDFs on Google Drive read PDF documents from web pages,and download to desktop or save to Google Drive this can replace Chrome's default PDF viewer, there are free, premium and Work versions available the premium version is $15.00 a year and the work version is $50.00 a year.

• Ocr, create searchable pdf.
• Unlimited e-Signature
• Unlimited Files to Split
• Unlimited Files to Merge