I am guessing that when disk space runs low, it automatically deletes the Spotlight index to make room for virtual memory. Then when space becomes available it reindexes. But I'm not sure about that.
Since my MacBook Air SSD is only 128 GB, I often work with little free disk space and the re-indexing drives me crazy.
I tried to disable Spotlight, remove its index and reindex. Also check filesystem and repair permissions. In diagnostic reports (~/Library/Logs/DiagnosticReports/) nothing about reindexing is mentioned.
You can say that I should control the amount of free space but also should be another way. Disabling Spotlight isn't the option.