I'd been in the same boat with fan speeds reaching 100% at 60 degrees unless AUTO mode was selected.

I probably have a workaround that I tested fine by making a profile and manually editing it.
 
1. Browse over to C:\Program Files (x86)\EVGA\Flow Control\Profiles
1. Make a new profile '1' in EVGA flow app.  This will create a new cfg file in above directory say CPUWB_0.cfg
3. Edit this file in Admin mode (I used notepad++) and change the below string

000100000000000600000000000000140000001900000020000000230000002A0000003C0000002E0000004B000000340000005A0000003C00000064

to 

000100000000000600000000000000140000001900000020000000230000002A0000003C0000002E0000004B000000340000005A0000003C0000004B

 4. Apply profile and monitor fan speed.
 
The above piece reflects the 60 degrees (3C is hex for 60) and 100% fan speed(64 in hex)
I changed the max speed to 4B (75%) and applied profile and it worked.
You may repeat and modify for other points manually.
 
NOTE: Opening fan curve would revert my changes.  So I only applied profiles to test out.  I haven't tested it out extensively so please try it out.
EDIT: attached pics for 60% fan speed and 100% fan speed profiles with spot at 60 degrees.
 
 

One and a half years later and this issue is still not solved. I just installed EVGA Flow Control for the first time to create a custom fan curve for the EVGA water cooler I have bought and I ran into this issue within the first 10 seconds. The custom fan curve in EVGA Flow Control is pretty much useless because of this bug. Is this the typical level of support EVGA provides for its products? 

I wouldn't really say 60 degree is a high temperature for modern CPUs; in fact, that is exactly why this bug becomes a problem because neither me nor most other people would want their cooler to run at full 100% when their CPU just hits 60 degrees. I always set my CPU fans to run at 100% when the CPU has hit at least 75 or 80 degrees. I ended up connecting the fan connectors of my cooler directly to my motherboard and creating a fan curve on my motherboard's BIOS which [obviously] does not have this bug; considering the age of the bug, there is probably no point in waiting and hoping for EVGA to fix this issue...

I just came here to say I am very disappointed in EVGA's software. I tried the hex edit and it didnt work, even setting the file to read only.
 
I now have to buy a splitter so I can run the 2 fans on the motherboard and control it that way. Very poor form, and will be making sure not to recommend this product due to software.
 
And I thought precision X was bad!

Sad. Still experiencing this bug. Will be actively telling people not to purchase evga coolers because of this issue(and the 3+ year delay with no response or fix).