The effect of kernel operations on cache optimisations in a soft-core reconfigurable system is important for dynamic cache switching design. Considering kernel operations changes the subset of cache configurations that would be chosen for dynamic cache switching and also the decisions on when to cache switch. The results show that kernel operations can skew the effectiveness of application driven cache optimisations up to 20% over the original execution time. This skew is shown by mapping the performance of the applications both with and without kernel operations. The majority of the kernel operations is due to trap events generated by system calls like memory allocation or file reading. A cache configuration analysis methodology for fast searching of the design space is also explained and was used to find relevant changes due to kernel interference.