This one's really interesting...
So, I am getting lots of theese after including Ruins in my modpack:

[23:44:19] [Server thread/DEBUG] [com.github.abrarsyed.secretroomsmod.common.OwnershipManager/]: Saving ownership data for dimension 69 to C:\Users\Darkos\AppData\Roaming.minecraft\saves\Test\DIM69\SecretRooms-ownership.dat
[23:44:19] [Thread-5990/INFO] [STDERR/]: [java.lang.Throwable$WrappedPrintStream:println:748]: java.io.FileNotFoundException: C:\Users\Darkos\AppData\Roaming.minecraft\saves\mystcraft_profiling\DIM69\RuinsPositionsFile.txt_writing (System nie może odnaleźć określonej ścieżki)
[23:44:19] [Thread-5990/INFO] [STDERR/]: [java.lang.Throwable$WrappedPrintStream:println:748]: at java.io.FileOutputStream.open(Native Method)
[23:44:19] [Thread-5990/INFO] [STDERR/]: [java.lang.Throwable$WrappedPrintStream:println:748]: at java.io.FileOutputStream.(FileOutputStream.java:213)
[23:44:19] [Thread-5990/INFO] [STDERR/]: [java.lang.Throwable$WrappedPrintStream:println:748]: at java.io.FileOutputStream.(FileOutputStream.java:162)
[23:44:19] [Thread-5990/INFO] [STDERR/]: [java.lang.Throwable$WrappedPrintStream:println:748]: at java.io.FileWriter.(FileWriter.java:90)
[23:44:19] [Thread-5990/INFO] [STDERR/]: [java.lang.Throwable$WrappedPrintStream:println:748]: at atomicstryker.ruins.common.RuinGenerator$FlushThread.run(RuinGenerator.java:88)

Theese prints appear immediately after each other. Every time this log block appears my game freezes for around half second, then unfreezes for a second (until next block of logs appears in the console). This happens whole the time - it iterates through all dimensions the save posses and repeats the cycle. It happens both on old and fresh saves. Reproduced with and without FastCraft.

Full log: http://www49.zippyshare.com/v/Ulg2jGn7/file.html

Ps: "System nie może odnaleźć określonej ścieżki" is a polish equivalent to java's message: "The system cannot find the path specified"

Well "RuinsPositionsFile.txt_writing"... I can manually create this file in the specified path (tried just now), but... dont you think "txt_writing" is rather unusual extension?
Especially since "RuinsPositionsFile.txt" is already there.

It's so you won't have an empty file if MC or Ruins crashes while writing it. RuinsPositionsFile.txt_writing is in process of being written, upon completion RuinsPositionsFile.txt is deleted and ..._writing is renamed to it.

OK, I got the idea behind this.
WHOAH, WAIT: I've found it!
To myself: Next time when you test if file can be written under specific location, copy-paste the path instead of going there manually / using shortcuts.
So, back on the track:
There is small derp in path to a file: C:\Users\Darkos\AppData\Roaming.minecraft\saves\Test\DIM69
Notice missing backslash between Roaming and .minecraft.

Well, are there restrictions in place preventing Ruins from creating that file? Have you tried creating that file yourself?

Are you sure that didnt happen when copy pasting? The save folder reader is one of those things in the mod which never broke before

Oh crap, you are right. Missing backslash magically evaporated during copy-pasting :/
Just checked the log file - backslash is there.
It requires a bit more testing which cant be done now, but it looks like shutting down my AV prevents this bug from occurence.

Then i suggest you add your entire mc folder to the exclusion list, so that i can push trojans and viruses down your throat unopposed >:D