If you're running on a screen with only a resolution of 800x600 (as is common for virtual machines), then the inkscape window doesn't fully fit. Easy to test out xrandr -s 800x600 inkscape
Not a whole lot I can do on this one. Filed upstream at http://sourceforge.net/tracker/index.php?func=detail&aid=1719858&group_id=93438&atid=604306 though i wouldn't expect a quick response. I might close as WONTFIX if i don't hear anything from above... Did you know VMWare WS can adjusts the resolution of a Linux guest OS dynamically as you're resizing the window on the host ? It's pretty neat. Or is this happening with Xen VMs ?
Pretty sure VMware doesn't do that, but it's been a while since I've poked at it. This is with qemu/xen/kvm. But I know that VMware will come up as 800x600 by default due to a lack of monitor EDID info. It seems a little thing, but lots of reviewers end up testing in environments like this and if we're going to have inkscape on the default live image, then we probably do want to get this fixed if we can. If you need some help working on a fix, let me know and I'll try to carve a little bit of time up to poke at it or ask on fedora-devel-list
VMWare has supported randr resize since 5.0 (or is it 5.5?), though you need to compile the guest toolbox, which requires the any-any patch on FC-6. I use workstation 5.5.4 a lot on FC-6 host to test my fc-5 and fc-7 packages. Just maximize the console window and bam the guest resizes automatically. Anyways. The windows size limitation here are the horizontal and vertical toolbars. Since this is gnome, you can drag them out of the window which will then let you resize the window down to the menu width. To have the toolbars "compressible" (as in thunderbird for example, the masked toolbar buttons become available in a small submenu on the right of the toolbar) will require some non-trivial gtk hackage to improve the custom widgets inkscape is using for their toolbars. I don't think they use the standard GtkToolbar (it's compressible by default, but has many undesirable restrictions). I think this discussion needs to happen on the upstream mailing list, let me post something quick.
Update: upstream bug is http://sourceforge.net/tracker/?func=detail&aid=1469554&group_id=93438&atid=604306
In 0.46pre1 the window doesn't fit even into 1024x768. https://bugs.launchpad.net/fedora/+source/inkscape/+bug/168648
This should probably be closed as WONTFIX
Inkscape windows fits to 1024x768 with small icons (default in Fedora). 800x600 will only be fixed if someone implements collapsing of vertical toolbars, similar to ones present for horizontal ones (being discussed upstream). If you really need to run it at 800x600, detach the vertical toolbar.