AutoInvoice will load tax line only if you have successfully. linked the TAX line to it's Invoice line.
The TAX lines will be ignored if it cannot be linked with Invoice Line's. To link Tax Line with Invoice Line you must use the Line Transaction Flexfield.

The segment values of the line transaction flexfield uniquely identify any given line in the
RA_INTERFACE_LINES table. Use the following example to load TAX lines attached to Invoice Line:-
 

Attributes	Line	Tax Line
INTERFACE_LINE_CONTEXT	'STD. ORDER'	'STD. ORDER'
INTERFACE_LINE_ATTRIBUTE1	'1000000'	'1000000'
INTERFACE_LINE_ATTRIBUTE2	'01'	'01'
INTERFACE_LINE_ATTRIBUTE3	'LINE'	'TAX'
LINK_TO_LINE_CONTEXT	null	'STD. ORDER'
LINK_TO_LINE_ATTRIBUTE1	null	'1000000'
LINK_TO_LINE_ATTRIBUTE2	null	'01'
LINK_TO_LINE_ATTRIBUTE3	null	'LINE'

The INTERFACE_LINE_ATTRIBUTE1 is an order number, INTERFACE_LINE_ATTRIBUTE2
is the Order line # and INTERFACE_LINE_ATTRIBUTE3 is LINE_TYPE invoice lines and tax lines.

The combination of the three INTERFACE_LINE_ATTRIBUTE's makes each row in the
RA_INTERFACE_LINES unique, and the LINK_TO_LINE_ATTRIBUTE's are used to link this TAX line to INVOICE LINE.