You might be getting some conflict between the name and class of the two conkies - when conky refreshes, it's like reopening the window (app).
Use both lines in each conkyrc and give them unique class and names
own_window_class <unique class #1>
own_window_title <unique class #1>
own_window_class <unique class #2>
own_window_title <unique name #2>
you can also try to comment out the line
so that each conky window is fully decorated, then when you have them positioned where you want them, use the fluxbox window menu to remember their positions etc ... and auto write to the ~/.fluxbox apps file. Then uncoment the line to remove the decor.