One point to keep in mind while using the ADC in autoscan mode being triggered by the external pin (CNVSTR) is to make sure that the Single Trigger enable is not set to 1. Setting STEN = 1 would imply that a single trigger is required to complete the whole autoscan sequence. But, the motivation for having an external conversion start is to get a sample at an exact instance of time while the idea behind having scan mode is to measure contiguous channels. Since these are mutually exclusive requirements, external convert start is not supported in single trigger mode.
If STEN is set to 1 and the ADC is used with external convert start to autoscan channels, then the external channel will trigger the ADC intermittently. For example -
If a software/hardware redesign is not possible, one alternative that can be used in this case is to trigger a timer with the external convert and use that timer overflow to trigger the ADC in single trigger mode.