Where's the PARTITION BY Company part of your query? PARTITION BY is analogous to GROUP BY... and it seems to be missing, so the totals/counts won't "restart" when the Company changes.

Should it not be... Note the "PARTITION BY Company" in both calculations

SELECT Company

,[Revenue Year]

,[Revenue Amount]

,CASE

WHEN COUNT(*) OVER (

PARTITION BY Company

ORDER BY Company

,[Revenue Year] ROWS BETWEEN UNBOUNDED PRECEDING

AND CURRENT ROW

) > 2

THEN AVG([Revenue Amount]) OVER (

PARTITION BY Company

ORDER BY Company

,[Revenue Year] ROWS BETWEEN 2 PRECEDING

AND CURRENT ROW

)

ELSE NULL

END ThreeMonthRunningAvg

FROM YHL.NAICS_Company_Revenue

ORDER BY 1

,2