1) when did you last do inlet maintanance? (How old is the septum)
2) what temperature are you running the FID and are the air and hydrogen at the vendor reccomended flow rates?
3) are you injecting manually or using an autosamper?
4) do the retention times change?
5) If you make an injection with something that will not be lost to actve sites (like some parrafins) do you have the same kind of response problems?
6) Are this GC and column used for any other kinds of analysis?
My thinking here: something like 80% of GC problems are with the inlet system. Very often a leaking septum is a reason for loss of sensitivity (by sample escaping from the instrument!).
Active sites in the inlet or column can be a problem (and yes, with a packed column - you do not have the complex inlet that you find in capillary). Garbage on the glass wool can mess up an analysis - or failure to use deactivated wool - or handling deactivated glass wool too roughly, and breaking it up a bit to give lots of active surface, can also mess up an analysis. So a check with compunds not llikely to be affected by active sites can help here.
FID conditions and temperature - in fact all of the parameters need a check. Someone, who I will not name - lest I embarass my self

- has been known to quickly fix a parameter and then discover that whatever got entered into the instrument went somewhere else - only because the intended parameter did not get changed. Small errors like this can only be found by sitting down with the method parameters and checking them all.
Check gas flow into your instrument. Be sure that you have pressure at the back of the instrument that is at least 20 psi over the regulated pressure in the instrument. Regulators need pressure across them to work properly. I've seen a lab with adequate pressure at the cylinder, but about 10 to 15 meters of 1/8" tubing running from the cylinder to the instrument - with various T's splitting gas flow off to other instruments. Long story short. The instrument at the end of the line was starved.
Retention time changes indicate a problem in the instrument. And if they are varying, we need to ask more questions -- but know where to ask.
And the question about the instrument being used for other kinds of analsis -- given the nature of the compunds you are trying to analyze, residues left on the head of the column from other kinds of samples could affect your analysis.
And last question, while I am thinking of it:
7) Have you protected the samples from evaporation - multiple injections from the same autosampler vial over time will result in a change in the sample. The ether will evaporate through the punctured septum.
Let us know
Don