Has your ticket been a SQ ticket and SQ flight numbers?

Finding out the correct Fare letter on flights that run under a codeshare number is tricky.

For example you have a Lufthansa ticket from Frankfurt to Singapore and onwards to Kuala Lumpur. The ticket might show Z for the segment from FRA to SIn and Z for the segment from SIN to KUL - However these are LH fare codes. Whenever codeshare flights are involved there is a mapping of fare codes from the marketing carrier to the operating carrier - and mostly that is where the mileage differnces are coming form.
In the example above the LH Z-farecode (which is the second lowest discount business fare code) could be mapped to a SQ D-farecode (discount business farecode on SQ) - which means not 135% earning but only 125%

The TK mileage calculator spits out 1594 miles for the distance SIN-HKG (100% earning)

SQ high priced business class segments (Z,C,J) earn 135% mileage -> 2152 miles
SQ discount business class semgents (D, U) earn 125% mileage -> 1992 miles

So my guess is that your segment must have been a U or D fare segment. Then the TK calculations are correct.