Ever noticed that Auto Tone performs slightly different adjustments when applied during import as opposed to when applied in the Develop module? I've just run some experiments using LR 5.7.1 Camera Raw 8.7.1 using Canon CR2 images. 3 out of 4 test images

Question

Original Images after applying Auto tone in the develop module
Image
14BD3911.CR2
14BD3912.CR2
14BD3913.CR2
14BD3914.CR2
Exposure captured
Under
Over
Slightly over
Under
WB Temp (as shot)
2300
2300
6650
6650
WB Tint (as shot)
+7
+7
+6
+6
Tone Exposure (auto)
+2.9
+0.5
+0.5
+1.9
Contrast (auto)
+4
-3
-17
+6
Highlights (auto)
-48
-45
-11
-10
Shadows (auto)
+48
+45
+11
+10
Whites (auto)
0
0
+23
+29
Blacks (auto)
-7
-6
-14
-6
Images imported with LR General Preset Auto Tone
Image
14BD3911-2.CR2
14BD3912-2.CR2
14BD3913-2.CR2
14BD3914-2.CR2
Exposure captured
Under
Over
Slightly over
Under
WB Temp (as shot)
2300
2300
6650
6650
WB Tint (as shot)
+7
+7
+6
+6
Tone Exposure (auto)
+2.9
+0.5
+0.5
+1.9
Contrast (auto)
+4
-2
-17
+6
Highlights (auto)
-48
-45
-12
-10
Shadows (auto)
+48
+45
+12
+10
Whites (auto)
0
0
+22
+29
Blacks (auto)
-7
-3
-12
-3

Answer 1

I received two email replies (BriPhoto & Rob Cole) to my above post, which are now missing here. I only mentioned Auto WB because of this statement in your PDF posted here Shared Cat:
"Apply auto WB and Auto tone to an unmodified photo and note the changes.
Apply auto WB and tone to another photo with very different exposure and tone and note changes to confirm that changes are different and do depend on the content of the photo being operated on (assumption)."
You are now saying:
"However, in this case we are talking about the SAME raw file, imported from the camera's CF card twice. One is imported with no preset, then the Auto Tone preset applied, the other is imported with the Auto Tone preset set in the import module. Both files have the SAME WB setting (As Shot) and the same Temp and Tint, as you would expect. The only differences (in LR) are in the tonal values."
I repeated Import of the two copies of your 14BD3913 CR2 file (14BD3913.CR2, 14BD3913-2.CR2) following the above procedure. The Tone values are identical for both using LR5.7 on my Windows 7 SP1 system. I cannot duplicate your issue as outlined above.
Is this the Auto Tone preset you are using on Import?
Two other things you can try:
1) Reset your LR Preferences file:
http://members.lightroomqueen.com/Knowledgebase/Article/View/1148/198/how-do-i-delete-the- lightroom-preferences-file
2) If that doesn't correct the issue I would try uninstalling LR5.7.1, delete the LR Preferences file, and then reinstall LR5.7.1 using a fresh download.