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as an infamous programmer quote: that's weird! :)

can you give some more details on your system and environment? the config.log file would be interesting to start looking.
what distro? g++ version? etc.

try again from scratch, please. from the source tree:

./autogen.sh clean
./autogen.sh
./configure [--prefix=...]
make [lv2|jack]

note that the brackets meaning optional command arguments; try some options, one by one, and each time make sure you start from the top.

hth.
seeya.

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