@Liposuction Please tell me the config you have?
Are Lion and Windows installed on the same disk?
If so, is it on an MBR or GUID Partition Table?
If it is MBR, I would use EasyBCD and add a boot menu option for the Windows Boot Manager. I am not sure if we are allowed to discuss an MBR patch, so I may have to erase this. Does anyone know if this is Kosher?
If it is GUID, I would use Chameleon and make sure to set my whichever partition you want (Windows or Lion) to be the default partition. I used this up until a week ago and it did the job well.
If you are not hiding any volumes from the bootloader, there should be no reason for it to disappear. I did notice when I had an NTFS volume on my media drive that was not hidden I would sometimes see it appear and disappear. When I put Lion and Windows on the same disk I don't get the disappearing volume, but I do have the thing where my Windows never fully shuts down.
Good luck!!
P.S. If a guide is what you are looking for, I am sure there is one mixed in this entire site, or you could go to my blog. I think I have a pretty thorough guide on how to do it.