My first suspicion would be your sample solvent is allowing material to precipitate on the column or guard column or even in the injector.. Is your sample completely  dissolved in the initial mobile phase?. Does the the sample concentration remain completely soluble in the initial mobile phase whilst at the autosampler temperature for several hours?. 
If you inject a series of larger volumes of high % MeOH/Water blanks, do your carryover peaks get larger than normal, and then reduce?. What happens if you increase column temperature by 5 - 10C.  
Allow the column to rinse at 50:50 for longer at the end of the run before injection, just to confirm it is carryover that you are seeing. 
I would not bother with the nitric acid clean, at this stage, because the contamination is most likely either in the injector or on the front of the colunm ( which obviously isn't cleaned with nitric acid ). 
You can also prewarm a sample vial of final mobile phase, and quickly inject the largest possible volume several times to try and rinse the injector, using a short isocratic run of 50:50 mobile phase..
It possible something else in the sample is binding to the carry
over, so ensure that the problem doesn't happen with the standards.
If you dilute the sample with mobile phase, and inject a sample then a few blank injections of final mobile phase,  does the carryover decrease with each injection?. 
Are your wash solvents sufficiently aggressive to rinse material from the injector?. What happens if you try a new column.
Another cause could be a faulty injection system, but that should show up in other analyses.
Please keep having fun,
Bruce Hamilton