Prices at the consulate in Penang is RINGGIT!! Not Baht. and ya, it's more than you pay in, for example, Laos, where you pay in Baht because of the conversion rate. Even if you went to the consulate and did it yourself, you'll have to pay more than you would at the embassy in Laos.
METV - 60 days each entry within the valid period of the visa (6 months)
*each entry can be extended at immigration by 30 days for 1900 baht.
Get a SETV and you can stay for 60 days without worrying about it. If you decide to go out of Thailand and come back in, you can then just enter on an exempt visa which will get you 30 days at no cost. Seeing as you're only staying for 2-3 months, that's what I would do. If you KNOW you're going to go out of the country within 30 days of arrival, then don't get any visa and come in on the visa exempt entry getting you 30 days (which can be extended by 30 days at immigration office within Thailand for 1900 baht).
Note: you are only allowed two exempt entries by land crossing per year but there is no limit if you fly in each time.
Did you put your visa number on your arrival form? Happened to me and it was because I forgot to put the visa number on the form. However, I noticed right away.