On page 168 of a remedial law reviewer, vol. 1, 2016 edition:
Section 7, Rule 141 of the Revised Rules of Court actually requires docket fees even for compulsory counterclaims. It seems this was not so before A.M. No. 04-2-04-SC.
I searched high and low for a copy of the A.M. but could only find references to it.
In Korea Technologies Co., vs. Hon. Lerma,
G.R. No. 143581, Jan. 7, 2008, the SC made a definitive ruling:
On July 17, 1998, at the time PGSMC filed its Answer incorporating its counterclaims against KOGIES, it was not liable to pay filing fees for said counterclaims being compulsory in nature. We stress, however, that effective August 16, 2004 under Sec. 7, Rule 141, as amended by A.M. No. 04-2-04-SC, docket fees are now required to be paid in compulsory counterclaim or cross-claims.
The "not" could just be a typo and could readily be changed to "now" and everything would be all right. But the quoted jurisprudence would pose a problem.
Update 30 May 2017: After listening to Prof. Tranquil Salvador discussing the jurisdictional importance of docket fees it seems the reviewer is correct after all.
OCA Circular No. 96-2009 dated August 13, 2009 says that in a revised issuance of
Korea Technologies the second sentence in the above-quoted paragraph (which I emphasized in blue letters in this update) has been deleted.