There are some pitfalls possible.
one usual is:
After switching the input-mux you'll have to discart one measurement when running in countinuos mode.
best would be to upload your project here to let us have a look at and see if everything is o.k
To do so:
Build -> Clean Project
File -> Create workspace bundle(minimal)
and then upload the resulting zip-archive here.
Don't use "Continuous" mode of conversion when you are muxing the input of ADC. Use "Multi-Sample" mode of conversion if resolution <= 16 bits or "Multi-Sample Turbo" if resolution > 16 bits.
Kiku, there are no modes (except free-runnung and triggered) for the SAR-ADC. because it doesn't use a filter.
I'm still awaiting the project uploaded here to have a look at.
To do something right is one way, do perform something wrong, there are several ways ;-)
Are you using Triggered or free running mode?
If you are using multiple channels, then you need to use triggered mode.
The problem you will face if you use free running mode is after reading a converted value, a stray conversion would have started before and issuing a StopConvert( ) API. This will result in cross talk between two channels and hence result in corrupted values.
Using trigger mode on the other hand will allow only one conversion upon request, thereby avoiding cross talk between two channels.