Just a couple of thoughts regarding your situation....
An annual annalysis is a bit of a waste if you are analysing for machinery health. The interval between samples is too long. You could easily have a failure between samples. If you were analysing with the intent of optimising your oil change interval then 1 year might be fine. My question to you is what was the lab asked to analyse for, were you specific as to what you were trying to accomplish. Was the lab asked if they had any background with the data interpretation of your specific equipment? Was there an ongoing communication with the lab when you were seeing these issues you mentioned. Something to realise is that some (most?) labs make their money with volume. They do not necessarily have anyone performing the interpretation of the data from analysis of your equipment that has any previous mechanical background or has any knowledge about your operational conditions. This is changing with the current avaliability of certification programs.
Sometimes you get someone who sells you a particular analysis package and it get's used as a catch all for all of your equipment. Unless you get specific with your request to the lab and ensure that the lab does indeed have the expertise to interpret the data, you could very well be wasting your money.
Personally I wouldn't be satisfied in trying to develop some meaningfull data and look at the trends unless I had at least 8 samples a year for something that was running over 6000 hours a year. At least until I got some baseline information from which to base an interpretation.
So did you miss something, only the realisation that the lab looked at what they had assumed the equipment to be and with the expertise they had to interpret the results.
If you wanted to start over again and probably save some money then contact the OEM and ask them for their baseline oil analysis recommendations.
Running an oil change @ 1000 hrs or 6 times a year X 36 gallons @ $5. gal = $1000./year. Or 12 oil samples and analysis @ $20 each = $240./year. Plus the oil analysis SHOULD give you information on the internal health of the machinery as well as the health of the lubricant.
hope this helps.......
PS... oil analysis works it can be VERY cost effective in minimising unplanned downtime, and secondary damage. Don't let this experience deter you.