Yep, it's simply Autotools not liking to use a different version of one of its tools to update an existing build system (likely because they know they often show slight incompatibilities that can lead to more serious breakage in some more exotic use of them).

The only solution I know of is to manually re-generating the build system with the new version as you and @elextr did, either with autogen.sh or directly with autoreconf.

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