I miss capturing data during that period.The problem is that write latency for SD cards can occasionally be very long. This is caused by various housekeeping functions in the SD card.
SD cards must erase flash before writing. SD cards perform wear leveling to increase the life of the SD card.
You must separate data capture from writing to the SD card and buffer data waiting to be written.
You can capture data in an interrupt routine like this example http://forum.arduino.cc/index.php?topic=228549.0 .
You can use a small RTOS like the nilSdLogger example in NilRTOS https://code.google.com/p/rtoslibs/downloads/list NilRTOS20130720.zip.
Your current program will have so much time jitter that there is no point in logging data this fast. The information in a time series depends as much on the accuracy of the time of a data point as the accuracy of the value.
Many articles have been published about time jitter noise. Google for "time jitter noise adc" for articles relevant to logging analog data.
If your data set is small, you could use a RAM disk http://forum.arduino.cc/index.php?topic=229485.0 or http://forum.arduino.cc/index.php?topic=236038.0. You will still need to solve the time jitter problem.