I don't own a thinkpad and cannot tell precisely why there is a difference in fan speed in the two cases. Regardless it seems the system is running too hot even with the higher fan speed.
However, I did get significant cooling of my laptop using
tlp. Try installing it as described here. You will have to purge
laptop-mode-tools package if it is installed on your system else tlp will refuse to start. Since it was originally written for thinkpad laptops, it should work even better for your case. Note the two optional thinkpad packages mentioned on the page which could further help for thinkpad.
If the above does not help for your case, then you can enable intel p-state available in recent kernels. Enable it as described here. I don't use thermald as mentioned on that page since I did not have overheating problem, and I will not suggest trying that given what it says on that page about the state of thermald. Check pstate is getting used correctly:
cat /sys/devices/system/cpu/*/cpufreq/scaling_driver should show
intel_pstate. Try setting the governor to powersave for both AC and Battery in tlp instead of cpufrequtils as mentioned on that page:
sudo gedit /etc/default/tlp, search for CPU_SCALING_GOVERNOR and add:
Then restart tlp:
sudo service tlp restart
Check if it has taken affect:
cat /sys/devices/system/cpu/cpu*/cpufreq/scaling_governor should show powersave
If even that doesn't work well for you, then you could try installing a newer kernel (as I have been using) which has better p-state implementation. This is really the VERY LAST RESORT if everything else fails to cool down the laptop. Get the debs from here:
http://kernel.ubuntu.com/~kernel-ppa/mainline/v3.15.5-utopic/. You will need amd64 packages (assuming you have 64-bit Ubuntu installation) for
linux-image-*-generic, linux-headers, and linux-headers-*-generic.
Additionally you could try installing the
thinkfan package for controlling the fan on thinkpads but I have no experience of using it so cannot provide any tips for the same. You can also check the howto's given here for thinkpads specifically those dealing with power management like this.
Edit: with tlp you may have to also explicitly disable ondemand/cpufrequtils for the "powersave" p-state governor to take affect as I mentioned above. See this.