Hi Andy,
Unless the work is progressing at an even pace throughout the entire project, the % complete - which is a duration measure - will not equal the % work complete. For example in the beginning of a project you may not have as many hours expended in each month as you may have later in the project when more resources join. So, you may have progressed 2% of the total duration, but because of backloaded resources, you have not consumed 2% of the total work. Look a the task usage view, add work to the timescaled portion zoom out and look at your work load per month.
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