Yes, this is an issue even if you kept 2003, as the system firmware addresses several key issues affecting stability and performance.  However, with 2008R2 and 2012, the latest firmware versions of all system firmware will be required for it to work properly (or at all) ... it is documented somewhere in the 2012 information I linked to previously.  Best just to update.
What is the most recent Windows server operating system you can load on this computer?
Poweredge 2900 (upgrading the OS from SBS 2003 question)