Ah, I did not understand your problem correctly.
A boot cd should not care about the partitions on a hard drive. Make sure that your BIOS is set to use a CD/DVD player as the primary boot device. Some bootCD's wait for a while for user interaction to start and without this interaction let the system boot normally from hard drive after this grace period. That could be an explanation for your problem with the Hirens BootCD.
The content of the Hirens BootCD is unknown to me, but I'll guess it contains a lot of software to repair broken systems as well. Going from that assumption, it is very likely that there is a software package on the CD that can show and/or edit partitions on any hard drive recognized by the BIOS.
Start that piece of software and check which partition is set to 'Active', as far as I know only primary partitions can be set to 'Active'. It is also not possible to set more than one 'Active' partition per hard drive and (by default) you cannot put more than four primary partitions on a hard drive. The 'Active' partition is used by he BIOS to start the Operating system. However, the Operating system will not be able to start the if the 'Active' partition does not contain any of the following files:
From these files only the 'boot.ini' file is easily fixed.
For example, this is the content of my boot.ini file (XP)
multi(0)disk(0)rdisk(0)partition(1)\WINDOWS="Microsoft Windows XP Professional" /fastdetect
default=multi(0)disk(0)rdisk(0)partition(1)\WINDOWS means: use this entry as the default Operating system
multi(0) means: single hard drive
rdisk(0) means: first available drive
partition(1) means: first available partition
\WINDOWS="Microsoft Windows XP Professional" means: default WINDOWS folder and name
/fastdetect means: important setting for NTDETECT.COM.
For example, this is how the content of your dual boot system would look like
multi(0)disk(0)rdisk(0)partition(1)\WINDOWS="Microsoft Windows XP Professional"
multi(0)disk(0)rdisk(0)partition(2)\WINDOWS="Microsoft Windows 2008 Server edition" /fastdetect
Above boot.ini file makes sure that Win2008 is started by default. More info
(Microsoft) about the boot.ini file