To use software SPI you must have edited SdFatConfig.h and changed MEGA_SOFT_SPI.
Go to about line 85 and change it back to the default:
#define MEGA_SOFT_SPI 0
The SPI will be much faster.
Unless you have a very high quality SD, you will have dropped data. Most SD cards have an occasional write latency of over 100 milliseconds.
Only the best card have sustained low latency and only when used with the multiple block writes as used in binaryLogger.pde.