I assume you are talking about WriteCounter( ) API for the fixed function Timer. This issue still exists with the current version of PSoC Creator.
Thanks, any idea when this would be fixed? or when would the next creator update would have this fixed?
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The s/w defect will be fixed in our next PSoC Creator release, which should be available on Early Access in May. Note that the fix only applies to PSoC 3. On PSoC 5 you should use a UDB-based Timer if you need to write the counter register.