I'm posting in Help subforum until I'm certain this is a software issue. I'm not sure if this is already known, but I don't find anything at Launchpad about it. If it turns out to be a bug, this can be moved to Software subforum. If there's a known fix, please let me know
Working in a document with default units set to px, I had made some paths with nodes placed precisely. I was wondering if I might want to use different units, so I changed my default units to cm. But before I changed the grid units, I decided it wasn't going to help, so I changed default units back to px. Now the ruler doesn't match the nodes' original placement. I made screenshots. My snipping tool, for some reason doesn't capture the mouse pointer, and neither does Prnt Scrn key. But you can see the tiny black arrow on the ruler, which shows the pointer position.
This is with units set to px. All screenshots are at 100% zoom.

Change units to cm, decide not to use cm, and change back to px. As long as Document Properties dialog is open, the ruler stays aligned with the original image. Shown here:

But as soon as Doc Prop dialog is closed, ruler becomes misaligned from original drawing, by what appears to be approx -10 to 15 px:

This is on Window 7, 64-bit and Inkscape 0.48.1. I've never noticed this before, but I don't use a grid, or non-px units very often. Note that I have not yet compared this misalignment to the X and Y positions (of the cursor/pointer) shown in the bottom, right corner of window. Also, note that this is all about the hoizontal, or X ruler. I haven't checked for the vertical Y ruler yet.
I don't know of a way to show this next part, except with a video, and I haven't learned how to make a video yet. The tiny black arrow, with the document in the same condition as the 3rd screenshot, changes it's horizontal position, when the mouse pointer is moved from the canvas to the ruler and back. So imagine the mouse pointer directly above the selected node, on the 300.00 px vertical line, and at the intersection of the topmost blue gridline (or anywhere along the 300.00 px gridline). As long as the mouse pointer is over the canvas, the black ruler arrow lies at 300.00 on the ruler. Of course that's what you would expect, except the 300.00 on the ruler is no longer aligned with the node placed precisely at 300.00 px. As soon as you move the mouse pointer from the top gridline (at 300 px) to the ruler itself, 2 things happen. One - the mouse pointer changes from Node pointer to Selection tool pointer (which I think is expected) (or maybe technically it changes to regular Windows arrow (which I use an enlarged version, that perhaps is the same size as the Selection tool pointer)). But more importantly, 2 - the tiny black ruler arrow jumps from 300 on the ruler to the real position of the pointer (which appears to be +10 to 15 px difference). Actually I just thought of a way to make still screenshots to show what I mean, if you need a visual.
The only fix I've found is to close the doc and re-open, and then avoid changing units. Or if I change units, leave Doc Prop open, which is not really feasible for the long run. Maybe I can't find a bug report, because this has been already fixed? Or more likely, I didn't use the right search terms
Thanks for your help