No, it doesn't mean you don't have Lyme. I had symptoms for 7.5 years before learning I had Lyme. My Igenex was also negative. I then had a DNA Connexions PCR analysis that was positive for Lyme and Ehrlichia.
Did you have any positive or indeterminate bands on the Igenex test?
IgM: band 41 Intermediate
IgG: band 41 Intermediate
Other tests by Lenco Diagnostic Lab (this is a regular lab, they don't specialize in Lyme):
Epstein-Barr virus: 8 (reference <0.8)
EBV ECA IGM ABS: <0.2 (reference <0.8)
EBV Nuclear IGG ABS: >8.0 (reference <0.8)
Lyme Disease AB: 0.05 (reference <0.90)
Mycoplasma IGM ABS: 0.19 (reference <0.90)
Toxoplasma Toxo IgG: 3.6 (reference 0.0 - 7.5)
Toxoplasma IgM /W RFLX CONFIRMATION
Toxo IgM: 0.2 (reference 0.0 - 8.0)
Lyme IgM ABS: 0.19 (=/< 0.90 - No detectable B Brurgorferi IgM Antobodies, Result does not exclude infection. An additional sample should be tested within 4-6 weeks if early infection is suspected).
So, out of those above I'm positive only for Epstein-Barr virus and EBV Nuclear IGG ABS.