Generally a 141 intermediate stage check is not considered to be a checkride. A part 61 student may have to repeat some maneuvers before mastering them, that does not count as a failure...there's no reason a 141 student should get penalized for an intermediate stage check should either.
On the other hand, an EOC check is a checkride...regardless of the BS that 141 people spout about how you can't "fail" a 141 checkride.
Especially after colgan, airlines are sensitive to failed checkrides. Eventually 141 checkride failures will be reported to the FAA just like 61 checkrides. But in the meantime there is a good chance that an interviewer could spot a failed 141 EOC in your logbook.