The way you state the problem, you seem sure the problem is the Windows Updates. I run a 128G SSD and a 2 TB secondary drive and have not seen that type of problem.
You don't give any info about your system. But I have to wonder why Windows 7 will not see the SSD if the HDD is plugged in? What SATA ports do you have the drives in, and are any of these ports special, like on another controller?
If you system appears to favor the HDD, a bootmgr is missing message would mean the system is looking in the wrong place for it. If you are running an MBR system, and you probably are, do you show an active partition on the HDD?
Have you gotten involved at all with the Intel Rapid Start install?
Pat mentions using Disk Management. If you would use the snipping tool to take a picture of the Disk Management window and attach using the paperclip on the advanced replies, it might help. Make sure and expand the window so we can see the comments about the different partitions.