Could you please keep a breakpoint on write on those variables and see if you could see the point at which it is getting updated ?
By "Breakpoint" do you mean an "if" code of some type or is it a feature in PSOC Creator?
Sorry for my lack of knowledge.
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A breakpoint uses the attached debugger/programmer to halt the executing code either on a specified line (Line Breakpoint) or when a variable is written or read (Data Breakpoint). There are also address breakpoints and Function breakpoints (to break at specified addresses in code or upon entry to functions respectively).
This can be very helpful for tracking down something in code that's misbehaving.
For line breakpoints, simply right click the line you want to break on in your code and choose "Insert Breakpoint". The line will be marked with a red circle. When debugging the code will halt on that line and you can look at the state of your variables and registers at that point.
For a data breakpoint, in creator, go to Debug>New Breakpoint>Variable Watchpoint.
You can then type in which variable you want to break on, and if you want to break when it's read/written/accessed.