I once had a weird FID issue where the signal suddenly went way up and didn't look like it was coming down. I looked at the jet and it was OK, restarted the instrument and then let it bake out for an hour and it was fine. The only real theory I had was that I had somehow pushed some of the material up out of the packed column but my coworkers were very skeptical so I'm not really sure what happened. This was a 6890 and it happened quite awhile ago so I don't remember many of the details but as far as I know having material come out of the column is pretty unlikely the way they are packed.
I did run into an issue one time where there was a small piece of broken capillary column sitting next to the jet. The FID signal was very high and jumpy, I found the piece and after that it settled down but its likely that if I had just let it sit for a few hours at high temperature all of the phase inside the little piece would eventually burn off and things would be OK again.
It is possible that you have a restriction in the jet which is causing a smaller than expected response. Changing the jet is very easy, if you haven't done it before follow these instructions:
Cool the FID to below 100 C, unscrew the 3 screws holding the top of the FID on to the base (this website shows an exploded parts view including the 3 screws I'm talking about
http://www.cobertassoc.com/Agilent-6890 ... -Detec.gif just unscrew them and pull the top of the FID off as one piece). Use a nut driver to unscrew the jet and then tweezers to pull the jet out. Put a new jet in and use the nut driver to tighten it (don't have to go crazy getting it as tight as possible just make sure its securely in there). Place the top of the FID back on and make sure you have it assembled correctly by checking the signal, if you see something between 2.0-0.0 pA its on there correctly. If you see 800089898729 or some other large number starting with 8 you have placed the top of the FID onto the spring that transfers the signal to the electrometer and you need to wiggle and adjust the top until it goes into place correctly.
Once its back together and screwed in tight (those 3 screws help ground the signal and its important that they are tight) heat it up to 300+ and let it sit for awhile to burn off any finger oils or other stuff that is on the jet and the signal should come back down to what it was before. Once it is equilibrated properly run your standard again and see if its any better. If the peaks are still small the problem is 99% the sampling technique (ie the syringe), the inlet, or your Y connector.
Where did you get the standard you are using? Did you purchase it or make it yourself?
Agilent has two FID standards that are very useful for troubleshooting. They both come in blue boxes containing 3 amber ampules of hydrocarbons (C14, C15, C16) in hexane and you should have some from when the GC was installed. I'm not sure if the method would translate well to your packed column but if you have the column that came with the GC (HP-1 30 m x 0.25 mm x 0.25 um) you could install it and try the Agilent standard. If you try this it would be much easier to tell where the problem is and how severe it is.
Let us know if you need more help

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