When two chains of command blocks are merged, rest of chain is executed only once.
Might be WAI as lock for command block loops, but i don't know for sure.
When you execute two chains (like in screenshot), one chain will be executed with middle section, after that second chain will execute without merged section.
Impulse command blocks are set to /say SL or SR (start left/right)
Separated chain commandblocks are set to /say L1, L2, L3 and R1, R2, R3. Middle 3 ones are /say M1, M2, M3.
Result of placing redstone torch in between is:
[@] SR
[@] R1
[@] R2
[@] R3
[@] M1
[@] M2
[@] M3
[@] SL
[@] L1
[@] L2
[@] L3
(M1, M2, M3 are not repeated after L3)