SQL 2005 Express resources

Well I am running SQL 2005 Express on windows 2003 sp2 with a P4 3.4Gh (with hyperthreading), 2GB ECC RAM.
I am running software that connects to SQL and reads/saves data.
One of the programs which is CPU hungry manages data and the other manages the SQL connection and reads/saves the data.

My problem is that I am recieving an error that usually means connection to SQL is lost, this tends to be because the CPU hungry application is denying SQL from functioning.

However the annoying thing is the CPU use rarely passes 45% and in a another test environment never passed 5%. RAM is the same, consumption is less than 35%.

I am wondering if there is a problem with the hyperthreading CPU?

Any ideas?
Thanks a lot!