Hmm, how high is your KPS? Because Training Speed is affected by ln(KPS) * 2. The value is subtracted from the training speed after upgrades.
For example: the base speed of 1200 seconds gets reduced to 900 seconds after upgrades, achievements and other Bonuses.
Let's say your KPS 1e100. ln(1e100) is about 230.26, times two is about 460.52.
Subtract this value from your training time and you're left less than 440 seconds.
Now I imagine your KPS is much higher, but that's just an example :D