The tolerance (± 5 % ) for the + 5 V is based on the Min/max voltages for TTL logic chips.
For the +12 V, voltages below 11.4 make the CPU voltage regulators on the MB work harder and can over heat. For this reason I use 11.6 V for a Min on the +12V. Slightly above the 12.6 (ie up to 12.8 V) is normally OK.
The +3.3 V use to be used for the Ram, but newer systems (past couple of years) use the +12 V (Could also use the +5)to step down to the required DIMM voltage. So I'm not really sure whate the 3.3 is used on current systems (I've heard that some of the Newer HDDs may use it - have not confirmed but voltage is included on SATA power connectors.) The 3.3V line is also used for the 1.5V AGP voltage (Again this was for older systems). Some PSUs do not provide good regulation when the current is below what the manuf is expecting and may be the reason it is out of spec.
You didn't mention which MB/system you have so it's hard to say. The +10 % on 3.3 is Probably Not a problem (in itself). UNLESS your MB is infact classing it as Over voltage and not allowing the "I'm OK" signal