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I gave up with the online system and applied for a paper visa in Astana. Sumbitted my documents on the standard visa, not e visa, website and was told to not bother waiting for "pre-approval", just to come to the embassy where they would go through the details with me.
I submitted my docs on a Friday and went on a Tuesday as the Monday was a holiday for them. Waited about 20 mins and then went into the consular office, very informal atmosphere with a super friendly and chatty lady, she spoke fluent English and reassured me of the simplicity of the whole process - she was shocked when I told her about all the e visa issues people were having. Told me to return on Friday, which I did, and after waiting for a good couple hours outside the office (where you're not allowed your phone, so bring a good book!) I was invited in for a final review of my trip details. Visa printed there and then.
Visa cost was 38000 KZT, a reasonable price. I paid in dollars, cash only! At the entrance to the embassy you have to surrender your phone to the Kazakh police who will also note down your passport details, when collecting your passport from the embassy make sure to bring a photocopy of it to enable you to get past the checkpoint.
Working hours of the consulate department are 9am to 6pm Mondays to Fridays with lunch break from 1pm to 2pm. However they do not publish any deviances from these hours, so I came on Monday with no knowledge of the national holiday and was turned away, and on Friday was made to return after 2pm as for some reason they were only working after then. Also don't bother with their website or email address - just turn up and rest assured all will be fine!