Solution:
For Error ID 67:
Branching to any of these timer instructions may provide unpredictable results in terms of starting and stopping these timers.
A simple workaround to this issue is to add a "NOP" instruction in front of each of these timer instructions which are also branch targets. After adding the "NOP", change the targets from each of the branch instructions to the "NOP" steps. The branch instructions which need to be updated, are shown in the error message received during compilation in version 6.2 and later.
For Error ID 27:
Some of the logic outputs configured for I2C control are also used in the Sequence Controller which causes conflict. Try changing the "Digital Control From" in the "Logic Outputs" window. If it's used in the Sequence controller, select "PLD" instead of "I2C Register".
The PAC-Designer, version 6.2 and later, implements the correct behavior.