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If you're document isn't matching up with a website (I'm assuming this is the application) and you're not getting the last two pixels lining up, maybe just flattening your image and cropping those last two pixels out.

If you still want those pixels to be grading up to the end, you might have to pop back into your blending settings and change the colours on your gradient. Sounds to me like you may have missed it by just a little bit.

Short of that... maybe selecting the entire document, and stretching it to fit; it's a small enough change that it may not be an issue.