There's something about this version of the mod that changes the world's DayTime nbt data in the world's "level.dat" file.

Our world is very old (roughly 3.5 years old IRL), and we've had it going for a long time so the DayTime is extremely high, but this gets changed when the mod is started on the server.

Here is a before and after picture of the level.dat file (see "DayTime") 2 images here: http://imgur.com/a/dWAci

Here is the Stellar Sky debug info verifying the change… 2 images here: http://imgur.com/a/2rC9o

I'd inspect into it, but it seems that it might be a forge bug or bug with another mods.
Please post log.

I don't have log files from when that happened. To recreate the bug in your dev env, set your DayTime and Time nbt's in your level.dat of your test world, to something like 5247194381. Then start up stellar sky, show the debug info for the Year, Day, Tick… and then sleep in a bed. It should change after you sleep.

Yeah, it happens after sleeping for the first time. After that first time, it doesn't happen again… time continues to add up normally.

So this happens after sleeping?
EDIT: + I tried changing DayTime, and cannot find same error in dev env.

So had the time displayed on the screen also changed?

Yeah. The first image was from the moment I started up the world, and the second image is from after I had my first sleep.

What was your configuration settings?

This is my client config file: http://pastebin.com/iSqLsp9W
This is the server config file: http://pastebin.com/8eMJzqWA

Similar issue with Version 17.. where if I set both wake properties to False…. it subtracts ~2,000,000,000 ticks from DayTime and time runs backwards (or crashes if you have NEI installed).

It is intended feature. It should not work when both wake properties is false.
You should totally disable wake system of Stellar Sky to do that.

I misunderstood. I thought the wake system Enable/Disable… totally overrides the subset of wake alarms. Thanks!