Are you using a SPME liner? There are special narrow bore injector liners available for SPME. I have seen broad peaks like you describe when I used a Splitless liner instead of a SPME liner. 

Iodine containing  compounds are also light sensitive. Are you doing the SPME extractions in the dark to avoid decomposition of the iodine compounds. I had 250 grams of a pure vinyl iodide that I made decompose in a matter minutes while I was adding it to a reaction under the florescent lighting in the laboratory. My second attempt was done in the dark using a red safety lamp avoided the spontaneous decomposition. You can use amber colored glass sample vials and aluminum foil wraps to help minimized light exposure during SPME.

Negative, I am using a splitless, single taper, ultra inert liner. I have attached one of the graphs I am seeing (hopefully the liner will be the culprit!). We are trying to get iodo-methane/ethane down to the 200 ug/L range, and at first I would get a reading of either iodo-methane/ethane with the large peak, and now I am not getting anything iodo-related even with the peak. Would that have an effect on it as well?

I am not doing SPME extractions in the dark, however I do have my serum vials wrapped in aluminum foil and stored in the dark. Still getting positive readings for manual injections though, however i will start doing the injections/extractions in the dark.

Iodomethane and iodoethane are both very volatile (BP's 40C and 70C respectively) and very reactive. Any free amines or sulfhydryl's present in the serum can react like cysteine residues, epsilon amines of lysine residues and protein/peptide n-termini. You would have to work fast to extract these compounds before they can react with anything in the serum. Also you will not be able to heat the serum much over room temperature because the iodomethane (and to a lesser extent iodoethane) will volatilize back out of the SPME fiber at higher temperatures. When working with these compounds I noted that they are easily decomposed by exposure to air and light and readily absorbed onto and into organic surfaces like polyethylene microfuge tubes. I found that iodomethane actually absorbed into polyethylene plastics. I would suggest doing a liquid-liquid extraction (using butane or dimethylether) in glass tubes to extract and recover these compounds from serum.  Alternatively, you might be able to make a derivative of these compounds that can easily be extracted and analyzed. As for the reactivity of the iodo compounds, I suggest adding a low concentration of 2-mercaptoethanol or dithiothreitol  to your liquid standard and seeing if you can still see a low level signal. This might help establish whether or not you can recover these reactive compounds from serum.  

Thank you for your help! I will look into those methods