Apart from the points made above (I really like jwkrahn's idea), the non-linear time difference (either one of the files by itself is a lot faster than the two files together), could indicate that the files are big enough (and/or you were wasting enough memory) that you ended up having to use virtual memory (i.e. portions of your in-memory array had to be paged out to the system swap file).

The time drag when you're using swap will depend somewhat on what you do with your big array after it's loaded. If you're still seeing a serious runtime delay after trying the ideas above, your choices are: (a) put more RAM on the machine (use a machine with more RAM), or (b) figure out how to do what needs to be done without having all that stuff in memory at one time (database? DB_File? -- depends on what you need to do.)