I've dealt with this.
Actually in my experience, you were never supposed to knock out the background, you are always supposed to use it exactly as provided. (I've knocked it out successfully also) If you've gotten away with this in the past, it's because the printer didn't care enough about enforcing FSC's guidelines.
You have three options, each with its own risk/reward.
1) Print logo as according to guidelines, and have your piece look worse.
2) Push back with the printer and insist that they print the FSC logo your original bastardized way. See if they'd rather do that, or if they want you to shop the job around to someone who will. Cite this:
"where no unprinted white areas are available, in a printed item using standard or limited colors, a
transparent label may be used, allowing the label elements to be reproduced in black or white on a
background color that provides sufficient contrast.
For example: If the background of a printed item using full colors is red and it is technically difficult
to reserve a white area, the label elements may be reproduced in black or white on the red background providing sufficient contrast.
If in exceptional circumstances none of the above color options are possible, an individual solution
should be proposed to FSC via the certification body"
http://www.fscus.org/images/documents/lo...20V1-2.pdf
3) My preferred solution when it comes to the FSC logos: push back with the client and explain that the inclusion of the FSC logo as specified detracts from the design, which will have a much greater negative impact on the design of the piece, versus including it. Explain that no one knows what the FSC is or does.
Seriously, ask your client what "FSC" stands for and see if they can answer accurately. The logo has absolutely no worth to consumers. Unless you are designing for a client who is in, or related to the environmental industry and it's an absolute requirement, no one out there really knows what the FSC does or why it's a benefit. I've only worked with one client where the inclusion of the FSC logo was a must. After an explanation that they are spending a lot of money on the print job and that they should want it to look as best as possible, they generally agree. Have mockups of both with and without. That will make it pretty clear.