From reading I have done, the answer seems to be that hypothyroidism can affect liver enzymes. The 25 mcg of T4 is a small, starter dose. I expect that you are overdue for an increase, and that your Free T4 and Free T3 are too low in their ranges. We need for you to call and get your test results and reference ranges and post them in order for us to give you a better assessment of your status.
I had elevated liver enzymes for years due to untreated Hashimoto's thyroiditis. I found one of my lab results:
ALT 83 U/L (0 - 45)
AST 45 U/L (0 - 41)
Excerpt from World Journal of Gastroenterology - Liver in systemic disease...
"Thyroid disease
Patients with hyperthyroidism frequently experience liver injury, which may be caused by increased hepatocyte oxygen demand without an associated increase in hepatic blood flow. Liver injury can be either cholestatic or hepatocellular. Up to 64% of these patients show elevated serum ALP, and up to 35% show elevated ALT. Interestingly, only 17% of these patients show elevated GGT[17], and most of the increased ALP is bone-derived[87].
In contrast to hyperthyroidism, liver biochemistry abnormalities are less prominent in patients with hypothyroidism. However, modest elevations in serum AST and ALT have been reported in 84% and 60%, respectively, of patients with hypothyroidism[88]. Some patients may show low serum ALP[87], but their most characteristic symptom is ascites, which is caused by unknown mechanisms[87]. In addition, cholestatic jaundice has been described in case reports of patients with severe hypothyroidism[17]."