So, I think that means you have some old 4store binaries installed in another location, presumably /usr/local/bin/. Can you run 4s-update --version, and check it against git describe --tags. Both should be v1.1.4-207-g530264c, or something very similar.
I've just retested with --enable-dedup-insert, incase that was causing a bug, but I can confirm that it still works.
With DEBUG_MERGE and Git HEAD you should have had output that looks like:
ADD triple(uri<
http://uri.com/resource1>, uri<
http://uri.com/predicate1>, variable(t1)) to B1
ADD triple(uri<
http://uri.com/resource1>, uri<
http://uri.com/predicate2>, variable(t2)) to B1
Merge B1 to B0
After compact:
B0, join NONE, parent B0
P0 triple(uri<
http://uri.com/resource1>, uri<
http://uri.com/predicate1>, variable(t1))
P1 triple(uri<
http://uri.com/resource1>, uri<
http://uri.com/predicate2>, variable(t2))
Processing B0, parent is B0
execute 0/2: triple(uri<
http://uri.com/resource1>, uri<
http://uri.com/predicate1>, variable(t1)) DISTINCT
mmmms (_,_[f7d2d213bd234f98],_[d842c1cfc4e4d77d],?) -> 1
append all, result:
t1 t2
row order p-nb A00 D-1 p-n A00 D-1
0 0 4ce5342b423f766b null
1 bindings (1)
execute 1/2: triple(uri<
http://uri.com/resource1>, uri<
http://uri.com/predicate2>, variable(t2)) DISTINCT
mmmms (_,_[f7d2d213bd234f98],_[e0bcc1593adc4a1e],?) -> 1
old: 1 bindings
t1 t2
row p-nb A00 D-1 pun A00 D-1
0 4ce5342b423f766b null
new: 1 bindings
t1 t2
row p-nb A00 D-1 p-nb A00 D-1
0 null 373af919ca19a580
result: 1 bindings
t1 t2
row p-nb A00 D-1 p-nb A00 D-1
0 4ce5342b423f766b 373af919ca19a580
1 bindings (1)
Processing B1, parent is B0
skipping B1, no bindings
skipping B1, no bindings
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