When you type in a $100 expense and the HST tax code, does the journal entry report show you an expense of $100 or about $88.50?

If it is the latter, then you have set up your tax code as Tax included in Price = Yes.  When using a code like this you would normally enter $113 to get an expense of $100 plus $13 HST.  You would not enter $100 to get $13 in HST.

Setting the tax code to No for Included in price is likely what you were expecting.

The entry comes up as $100.

OK, but that really doesn't give us any information.

Is that what you typed into the amount field on the first row?

Is that the calculation of the sales tax for the row?

Is that the expense calculated for the invoice?

Is that the total of the invoice including sales tax?

Did you go back to the sales tax code set up to see if you marked the Tax included in Price column for HST as Yes or No?

When you added the Tax Code rate "13" did you then double on the tax code or description to open another dialogue box called Tax Code Details and enter the 13 under the rate?

After you entered the Tax Code rate "13" did you double click on the tax code or description to open another dialogue box called Tax Code Details and update the info including entering 13 under the Rate? 

The amount is $100 it calculate the tax at $11.50 for a total of $111.50.  The tax is not included on the tax code in the set up.

Then it just sounds like you entered the tax rate of 11.5 instead of 13.  Just go back to the tax code set up and change the rate.

I have discovered my problem.  I marked "yes" to the column "Is Refundable".  I have changed it and it calculates properly now.  Thank you for your help Richard.

Are you sure that was your problem?  Whether something is refundable or not does not change the calculation percentage.  That of course, is aside from the fact that HST is supposed to have Is Refundable set to Yes.

I still think it was the Included in Price column was set to Yes and your intent was to have it set to No.